UCSF
ZINC Item Suppliers, Protomers, & Similar Substances

Analogs

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Popular Name: (S)-N1-((1H-Benzo[d]imidazol-2-yl)methyl)-N1-(5,6,7,8-tetrahydroquinolin-8-yl)butane-1,4-diamine (S)-N1-((1H-Benzo[d]imidazol-2-y…

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Clustered Target Annotations
Code Description Organism Class Affinity (nM) LE (kcal/mol/atom) Type
CXCR4-1-E C-X-C Chemokine Receptor Type 4 (cluster #1 Of 2), Eukaryotic Eukaryotes 36 0.40 Binding ≤ 10μM
CXCR4-1-E C-X-C Chemokine Receptor Type 4 (cluster #1 Of 2), Eukaryotic Eukaryotes 206 0.36 Binding ≤ 10μM
CXCR4-1-E C-X-C Chemokine Receptor Type 4 (cluster #1 Of 1), Eukaryotic Eukaryotes 11 0.43 Functional ≤ 10μM
Z50607-1-O Human Immunodeficiency Virus 1 (cluster #1 Of 10), Other Other 5 0.45 Functional ≤ 10μM
Z50607-1-O Human Immunodeficiency Virus 1 (cluster #1 Of 10), Other Other 144 0.37 Functional ≤ 10μM
Z80295-1-O MT4 (Lymphocytes) (cluster #1 Of 1), Other Other 108 0.38 ADME/T ≤ 10μM

Physical Representations

Type pH range xlogP Des A‑Pol Apolar desolvation (kcal/mol) Des Pol Polar desolvation (kcal/mol) H Don H-bond donors H Acc H-bond acceptors Chg Net charge tPSA (Ų) MWT Molecular weight (g/mol) RB Rotatable bonds DL
Ref Reference (pH 7) 2.26 5.85 -47.99 4 5 1 72 350.49 7 ↓
Mid Mid (pH 6-8) 2.26 6.58 -83.64 5 5 2 74 351.498 7 ↓
Lo Low (pH 4.5-6) 2.26 7.64 -159.81 6 5 3 75 352.506 7 ↓

Analogs

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Popular Name: (S)-N1-((1H-Benzo[d]imidazol-2-yl)methyl)-N1-(5,6,7,8-tetrahydroquinolin-8-yl)butane-1,4-diamine (S)-N1-((1H-Benzo[d]imidazol-2-y…

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Clustered Target Annotations
Code Description Organism Class Affinity (nM) LE (kcal/mol/atom) Type
CXCR4-1-E C-X-C Chemokine Receptor Type 4 (cluster #1 Of 2), Eukaryotic Eukaryotes 13 0.42 Binding ≤ 10μM
CXCR4-1-E C-X-C Chemokine Receptor Type 4 (cluster #1 Of 2), Eukaryotic Eukaryotes 36 0.40 Binding ≤ 10μM
CXCR4-1-E C-X-C Chemokine Receptor Type 4 (cluster #1 Of 1), Eukaryotic Eukaryotes 11 0.43 Functional ≤ 10μM
Z50607-1-O Human Immunodeficiency Virus 1 (cluster #1 Of 10), Other Other 5 0.45 Functional ≤ 10μM
Z50607-1-O Human Immunodeficiency Virus 1 (cluster #1 Of 10), Other Other 9 0.43 Functional ≤ 10μM

Physical Representations

Type pH range xlogP Des A‑Pol Apolar desolvation (kcal/mol) Des Pol Polar desolvation (kcal/mol) H Don H-bond donors H Acc H-bond acceptors Chg Net charge tPSA (Ų) MWT Molecular weight (g/mol) RB Rotatable bonds DL
Ref Reference (pH 7) 2.26 6.23 -51.25 4 5 1 72 350.49 7 ↓
Mid Mid (pH 6-8) 2.26 6.94 -96.56 5 5 2 74 351.498 7 ↓
Lo Low (pH 4.5-6) 2.26 7.64 -163.81 6 5 3 75 352.506 7 ↓

Analogs

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Popular Name: [5-(4-methylpiperazin-1-yl)-2-[[methyl-[(8S)-5,6,7,8-tetrahydroquinolin-8-yl]amino]methyl]imidazo[1, [5-(4-methylpiperazin-1-yl)-2-[[…

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Clustered Target Annotations
Code Description Organism Class Affinity (nM) LE (kcal/mol/atom) Type
ACE-1-E Angiotensin-converting Enzyme (cluster #1 Of 1), Eukaryotic Eukaryotes 193 0.30 Binding ≤ 10μM
CXCR4-1-E C-X-C Chemokine Receptor Type 4 (cluster #1 Of 2), Eukaryotic Eukaryotes 0 0.00 Binding ≤ 10μM
CXCR4-1-E C-X-C Chemokine Receptor Type 4 (cluster #1 Of 1), Eukaryotic Eukaryotes 8 0.37 Functional ≤ 10μM
ENV-1-V Envelope Glycoprotein Gp160 (cluster #1 Of 2), Viral Viruses 2 0.39 Binding ≤ 10μM
Z50607-1-O Human Immunodeficiency Virus 1 (cluster #1 Of 10), Other Other 5 0.37 Functional ≤ 10μM

Physical Representations

Type pH range xlogP Des A‑Pol Apolar desolvation (kcal/mol) Des Pol Polar desolvation (kcal/mol) H Don H-bond donors H Acc H-bond acceptors Chg Net charge tPSA (Ų) MWT Molecular weight (g/mol) RB Rotatable bonds DL
Ref Reference (pH 7) 2.62 9.78 -81.92 3 7 2 63 422.577 5 ↓
Hi High (pH 8-9.5) 2.62 6.86 -13.96 1 7 0 60 420.561 5 ↓
Mid Mid (pH 6-8) 2.62 7.56 -73.43 3 7 2 63 422.577 5 ↓

Analogs

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Popular Name: N'-[[4-[[1H-imidazol-2-ylmethyl-[(1-methylimidazol-2-yl)methyl]amino]methyl]phenyl]methyl]-N'-methyl N'-[[4-[[1H-imidazol-2-ylmethyl-…

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Clustered Target Annotations
Code Description Organism Class Affinity (nM) LE (kcal/mol/atom) Type
CXCR4-1-E C-X-C Chemokine Receptor Type 4 (cluster #1 Of 2), Eukaryotic Eukaryotes 3 0.34 Binding ≤ 10μM
Z50607-1-O Human Immunodeficiency Virus 1 (cluster #1 Of 10), Other Other 1 0.36 Functional ≤ 10μM

Physical Representations

Type pH range xlogP Des A‑Pol Apolar desolvation (kcal/mol) Des Pol Polar desolvation (kcal/mol) H Don H-bond donors H Acc H-bond acceptors Chg Net charge tPSA (Ų) MWT Molecular weight (g/mol) RB Rotatable bonds DL
Ref Reference (pH 7) 2.93 16.04 -233.28 5 7 4 61 483.749 17 ↓
Hi High (pH 8-9.5) 2.93 13.05 -71.47 3 7 2 59 481.733 17 ↓
Hi High (pH 8-9.5) 2.93 13.54 -40.73 2 7 1 57 480.725 17 ↓

Analogs

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Popular Name: Plerixafor Plerixafor

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Clustered Target Annotations
Code Description Organism Class Affinity (nM) LE (kcal/mol/atom) Type
CCR2-1-E C-C Chemokine Receptor Type 2 (cluster #1 Of 1), Eukaryotic Eukaryotes 0 0.00 Binding ≤ 10μM
CXCR4-1-E C-X-C Chemokine Receptor Type 4 (cluster #1 Of 2), Eukaryotic Eukaryotes 7 0.32 Binding ≤ 10μM
CXCR4-1-E C-X-C Chemokine Receptor Type 4 (cluster #1 Of 1), Eukaryotic Eukaryotes 695 0.24 Functional ≤ 10μM
Z100081-4-O PBMC (Peripheral Blood Mononuclear Cells) (cluster #4 Of 4), Other Other 4 0.33 Functional ≤ 10μM
Z50607-1-O Human Immunodeficiency Virus 1 (cluster #1 Of 10), Other Other 4 0.33 Functional ≤ 10μM
Z50658-4-O Human Immunodeficiency Virus 2 (cluster #4 Of 4), Other Other 6 0.32 Functional ≤ 10μM
Z80076-3-O CEM-SS (T-cell Leukemia) (cluster #3 Of 5), Other Other 127 0.27 Functional ≤ 10μM
Z80295-7-O MT4 (Lymphocytes) (cluster #7 Of 8), Other Other 65 0.28 Functional ≤ 10μM
Z80865-1-O GHOST CXCR4 Cell Line (cluster #1 Of 1), Other Other 1 0.35 Functional ≤ 10μM

Physical Representations

Type pH range xlogP Des A‑Pol Apolar desolvation (kcal/mol) Des Pol Polar desolvation (kcal/mol) H Don H-bond donors H Acc H-bond acceptors Chg Net charge tPSA (Ų) MWT Molecular weight (g/mol) RB Rotatable bonds DL
Ref Reference (pH 7) -1.04 2.29 -156.31 9 8 3 89 505.82 4 ↓
Hi High (pH 8-9.5) 2.94 7.04 -11.84 1 10 0 126 459.499 7 ↓

Analogs

37996312
37996312
37998969
37998969

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Popular Name: WZ 811 WZ 811

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Clustered Target Annotations
Code Description Organism Class Affinity (nM) LE (kcal/mol/atom) Type
CXCR4-1-E C-X-C Chemokine Receptor Type 4 (cluster #1 Of 2), Eukaryotic Eukaryotes 0 0.00 Binding ≤ 10μM
CXCR4-1-E C-X-C Chemokine Receptor Type 4 (cluster #1 Of 1), Eukaryotic Eukaryotes 2 0.55 Functional ≤ 10μM
Z81252-3-O MDA-MB-231 (Breast Adenocarcinoma Cells) (cluster #3 Of 11), Other Other 5 0.53 Functional ≤ 10μM

Physical Representations

Type pH range xlogP Des A‑Pol Apolar desolvation (kcal/mol) Des Pol Polar desolvation (kcal/mol) H Don H-bond donors H Acc H-bond acceptors Chg Net charge tPSA (Ų) MWT Molecular weight (g/mol) RB Rotatable bonds DL
Ref Reference (pH 7) 2.65 8.37 -34.67 3 4 1 51 291.378 6 ↓
Hi High (pH 8-9.5) 0.51 2.82 -60.28 3 13 -1 183 531.446 7 ↓
Mid Mid (pH 6-8) 2.65 8.84 -71.14 4 4 2 52 292.386 6 ↓

Analogs

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Popular Name: AMD 3465 hexahydrobromide AMD 3465 hexahydrobromide

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Clustered Target Annotations
Code Description Organism Class Affinity (nM) LE (kcal/mol/atom) Type
CXCR4-1-E C-X-C Chemokine Receptor Type 4 (cluster #1 Of 2), Eukaryotic Eukaryotes 112 0.32 Binding ≤ 10μM
CXCR4-1-E C-X-C Chemokine Receptor Type 4 (cluster #1 Of 1), Eukaryotic Eukaryotes 10 0.37 Functional ≤ 10μM
Z50607-2-O Human Immunodeficiency Virus 1 (cluster #2 Of 10), Other Other 9 0.38 Functional ≤ 10μM

Physical Representations

Type pH range xlogP Des A‑Pol Apolar desolvation (kcal/mol) Des Pol Polar desolvation (kcal/mol) H Don H-bond donors H Acc H-bond acceptors Chg Net charge tPSA (Ų) MWT Molecular weight (g/mol) RB Rotatable bonds DL
Hi High (pH 8-9.5) 0.24 5.75 -168.11 7 6 3 75 413.634 6 ↓
Hi High (pH 8-9.5) 0.24 4.34 -107.26 6 6 2 70 412.626 6 ↓
Mid Mid (pH 6-8) 0.24 5.03 -177.16 7 6 3 78 413.634 6 ↓

Analogs

3978074
3978074
4245659
4245659
4245660
4245660
4467870
4467870
11592709
11592709

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Popular Name: Zidovudine Zidovudine

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Clustered Target Annotations
Code Description Organism Class Affinity (nM) LE (kcal/mol/atom) Type
KITH-1-E Thymidine Kinase (cluster #1 Of 2), Eukaryotic Eukaryotes 7000 0.38 Binding ≤ 10μM
CXCR4-1-E C-X-C Chemokine Receptor Type 4 (cluster #1 Of 1), Eukaryotic Eukaryotes 8 0.60 Functional ≤ 10μM
Z80295-1-O MT4 (Lymphocytes) (cluster #1 Of 1), Other Other 20 0.57 Binding ≤ 10μM
Z100081-2-O PBMC (Peripheral Blood Mononuclear Cells) (cluster #2 Of 4), Other Other 4 0.62 Functional ≤ 10μM
Z102020-1-O Porcine Endogenous Retrovirus (cluster #1 Of 1), Other Other 23 0.56 Functional ≤ 10μM
Z50459-2-O Leishmania Donovani (cluster #2 Of 8), Other Other 3400 0.40 Functional ≤ 10μM
Z50587-4-O Homo Sapiens (cluster #4 Of 9), Other Other 7 0.60 Functional ≤ 10μM
Z50594-1-O Mus Musculus (cluster #1 Of 9), Other Other 46 0.54 Functional ≤ 10μM
Z50607-1-O Human Immunodeficiency Virus 1 (cluster #1 Of 10), Other Other 9600 0.37 Functional ≤ 10μM
Z50609-1-O Simian Immunodeficiency Virus (cluster #1 Of 2), Other Other 12 0.58 Functional ≤ 10μM
Z50658-1-O Human Immunodeficiency Virus 2 (cluster #1 Of 4), Other Other 9 0.59 Functional ≤ 10μM
Z50664-1-O Rauscher Murine Leukemia Virus (cluster #1 Of 1), Other Other 23 0.56 Functional ≤ 10μM
Z50677-1-O Human Immunodeficiency Virus (cluster #1 Of 3), Other Other 9 0.59 Functional ≤ 10μM
Z50737-1-O Human Immunodeficiency Virus 3 (cluster #1 Of 1), Other Other 40 0.55 Functional ≤ 10μM
Z80052-1-O C8166 (Leukemic T-cells) (cluster #1 Of 3), Other Other 9 0.59 Functional ≤ 10μM
Z80071-1-O CEM-0 (T-cell Leukemia) (cluster #1 Of 2), Other Other 6 0.61 Functional ≤ 10μM
Z80073-1-O CEM-c113 (cluster #1 Of 1), Other Other 6 0.61 Functional ≤ 10μM
Z80076-1-O CEM-SS (T-cell Leukemia) (cluster #1 Of 5), Other Other 95 0.52 Functional ≤ 10μM
Z80193-2-O L1210 (Lymphocytic Leukemia Cells) (cluster #2 Of 12), Other Other 6180 0.38 Functional ≤ 10μM
Z80285-1-O MOLT-4 (Acute T-lymphoblastic Leukemia Cells) (cluster #1 Of 4), Other Other 6 0.61 Functional ≤ 10μM
Z80294-1-O MT2 (Lymphocytes) (cluster #1 Of 1), Other Other 6 0.61 Functional ≤ 10μM
Z80295-2-O MT4 (Lymphocytes) (cluster #2 Of 8), Other Other 10 0.59 Functional ≤ 10μM
Z80384-1-O PBL (Peripheral Blood Lymphocytes) (cluster #1 Of 1), Other Other 29 0.56 Functional ≤ 10μM
Z80516-1-O SUP-T1 (cluster #1 Of 1), Other Other 50 0.54 Functional ≤ 10μM
Z80566-1-O U-937 (Histiocytic Lymphoma Cells) (cluster #1 Of 2), Other Other 40 0.55 Functional ≤ 10μM
Z80683-1-O ATH8 Cell Line (cluster #1 Of 1), Other Other 400 0.47 Functional ≤ 10μM
Z80688-1-O B(EBV+) Cell Line (cluster #1 Of 1), Other Other 1 0.66 Functional ≤ 10μM
Z80721-1-O BxT Cell Line (cluster #1 Of 1), Other Other 55 0.53 Functional ≤ 10μM
Z80737-1-O C3H/3T3 (Embryonic Fibroblast Cells) (cluster #1 Of 1), Other Other 20 0.57 Functional ≤ 10μM
Z80760-1-O CFU-GM Cell Line (cluster #1 Of 1), Other Other 1500 0.43 Functional ≤ 10μM
Z80874-1-O CEM (T-cell Leukemia) (cluster #1 Of 7), Other Other 870 0.45 Functional ≤ 10μM
Z80897-1-O H9 (T-lymphoid Cells) (cluster #1 Of 2), Other Other 9 0.59 Functional ≤ 10μM
Z81072-2-O Jurkat (Acute Leukemic T-cells) (cluster #2 Of 10), Other Other 10 0.59 Functional ≤ 10μM
Z81223-1-O M Cell Line (cluster #1 Of 1), Other Other 15 0.58 Functional ≤ 10μM
Z81247-7-O HeLa (Cervical Adenocarcinoma Cells) (cluster #7 Of 9), Other Other 9 0.59 Functional ≤ 10μM
Z80874-3-O CEM (T-cell Leukemia) (cluster #3 Of 4), Other Other 700 0.45 ADME/T ≤ 10μM
Z80897-1-O H9 (T-lymphoid Cells) (cluster #1 Of 2), Other Other 45 0.54 ADME/T ≤ 10μM
Q72547-1-V Human Immunodeficiency Virus Type 1 Reverse Transcriptase (cluster #1 Of 6), Viral Viruses 6 0.61 Binding ≤ 10μM
Q72874-1-V Human Immunodeficiency Virus Type 1 Protease (cluster #1 Of 3), Viral Viruses 6 0.61 Binding ≤ 10μM
Q72547-1-V Human Immunodeficiency Virus Type 1 Reverse Transcriptase (cluster #1 Of 1), Viral Viruses 8 0.60 Functional ≤ 10μM

Physical Representations

Type pH range xlogP Des A‑Pol Apolar desolvation (kcal/mol) Des Pol Polar desolvation (kcal/mol) H Don H-bond donors H Acc H-bond acceptors Chg Net charge tPSA (Ų) MWT Molecular weight (g/mol) RB Rotatable bonds DL
Ref Reference (pH 7) -0.10 -3.76 -14.65 2 9 0 134 267.245 3 ↓

Analogs

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Popular Name: N4-[[4-[[(2-chloro-5-fluoro-pyrimidin-4-yl)amino]methyl]phenyl]methyl]-N2-(2-morpholinoethyl)pyrimid N4-[[4-[[(2-chloro-5-fluoro-pyri…

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Clustered Target Annotations
Code Description Organism Class Affinity (nM) LE (kcal/mol/atom) Type
CXCR4-1-E C-X-C Chemokine Receptor Type 4 (cluster #1 Of 1), Eukaryotic Eukaryotes 1 0.38 Functional ≤ 10μM

Physical Representations

Type pH range xlogP Des A‑Pol Apolar desolvation (kcal/mol) Des Pol Polar desolvation (kcal/mol) H Don H-bond donors H Acc H-bond acceptors Chg Net charge tPSA (Ų) MWT Molecular weight (g/mol) RB Rotatable bonds DL
Ref Reference (pH 7) 2.63 7.89 -37.41 4 9 1 101 473.964 10 ↓
Mid Mid (pH 6-8) 2.63 10.17 -102.59 5 9 2 103 474.972 10 ↓
Mid Mid (pH 6-8) 2.63 7.49 -9.96 3 9 0 100 472.956 10 ↓

Analogs

39908
39908
17175067
17175067
17175068
17175068

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Popular Name: Zalcitabine Zalcitabine

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Clustered Target Annotations
Code Description Organism Class Affinity (nM) LE (kcal/mol/atom) Type
CXCR4-1-E C-X-C Chemokine Receptor Type 4 (cluster #1 Of 1), Eukaryotic Eukaryotes 88 0.66 Functional ≤ 10μM
Z50606-1-O Hepatitis B Virus (cluster #1 Of 3), Other Other 2300 0.53 Functional ≤ 10μM
Z50607-1-O Human Immunodeficiency Virus 1 (cluster #1 Of 10), Other Other 910 0.56 Functional ≤ 10μM
Z50624-1-O Human Adenovirus Type 2 (cluster #1 Of 1), Other Other 3300 0.51 Functional ≤ 10μM
Z50658-2-O Human Immunodeficiency Virus 2 (cluster #2 Of 4), Other Other 690 0.58 Functional ≤ 10μM
Z50677-1-O Human Immunodeficiency Virus (cluster #1 Of 3), Other Other 800 0.57 Functional ≤ 10μM
Z80052-1-O C8166 (Leukemic T-cells) (cluster #1 Of 3), Other Other 125 0.64 Functional ≤ 10μM
Z80064-1-O CCRF-CEM (T-cell Leukemia) (cluster #1 Of 9), Other Other 22 0.71 Functional ≤ 10μM
Z80076-1-O CEM-SS (T-cell Leukemia) (cluster #1 Of 5), Other Other 50 0.68 Functional ≤ 10μM
Z80294-1-O MT2 (Lymphocytes) (cluster #1 Of 1), Other Other 994 0.56 Functional ≤ 10μM
Z80295-2-O MT4 (Lymphocytes) (cluster #2 Of 8), Other Other 300 0.61 Functional ≤ 10μM
Z80874-1-O CEM (T-cell Leukemia) (cluster #1 Of 7), Other Other 70 0.67 Functional ≤ 10μM
Z81020-1-O HepG2 (Hepatoblastoma Cells) (cluster #1 Of 8), Other Other 3200 0.51 Functional ≤ 10μM
Q72547-1-V Human Immunodeficiency Virus Type 1 Reverse Transcriptase (cluster #1 Of 6), Viral Viruses 51 0.68 Binding ≤ 10μM
Q72547-1-V Human Immunodeficiency Virus Type 1 Reverse Transcriptase (cluster #1 Of 1), Viral Viruses 31 0.70 Functional ≤ 10μM

Physical Representations

Type pH range xlogP Des A‑Pol Apolar desolvation (kcal/mol) Des Pol Polar desolvation (kcal/mol) H Don H-bond donors H Acc H-bond acceptors Chg Net charge tPSA (Ų) MWT Molecular weight (g/mol) RB Rotatable bonds DL
Ref Reference (pH 7) -1.06 -2.38 -18.62 3 6 0 90 211.221 2 ↓

Parameters Provided:

annotation.name = CXCR4_HUMAN
anotation.type = B10
page.format = summary
page.num = 1
filter.purchasability = purchasable

Structural Results Found: (before additional filtering)

SQL Query Was

SELECT DISTINCT(ci.sub_id_fk) AS sub_id FROM catalog_item AS ci INNER JOIN catalog AS c ON ci.cat_id_fk=c.cat_id INNER JOIN note AS n ON ci.sub_id_fk=n.sub_id_fk INNER JOIN annotation AS a ON n.anno_id_fk=a.anno_id  WHERE c.free = 1 AND a.short_desc LIKE 'CXCR4\\_HUMAN' AND c.purchasable IN (1,2,4,5)    LIMIT 50

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