UCSF

ZINC34849693

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Substance Information

In ZINC since Heavy atoms Benign functionality
September 29th, 2009 26 No

Popular Name: (E)-3-[1-(2-dimethylaminoethyl)-2-hexyl-benzimidazol-5-yl]prop-2-enehydroxamic (E)-3-[1-(2-dimethylaminoethyl)-…

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Download: MOL2 SDF SMILES Flexibase

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) 3.75 9.81 -65.33 3 6 1 72 359.494 10 ↓
Hi High (pH 8-9.5) 3.75 7.33 -18.5 2 6 0 70 358.486 10 ↓
Lo Low (pH 4.5-6) 3.75 10.09 -114.46 4 6 2 73 360.502 10 ↓

Activity (Go SEA)

Clustered Target Annotations
Code Description Organism Class Affinity (nM) LE (kcal/mol/atom) Type
HDA10-1-E Histone Deacetylase 10 (cluster #1 Of 3), Eukaryotic Eukaryotes 13 0.42 Binding ≤ 10μM
HDA11-1-E Histone Deacetylase 11 (cluster #1 Of 3), Eukaryotic Eukaryotes 11 0.43 Binding ≤ 10μM
HDAC1-2-E Histone Deacetylase 1 (cluster #2 Of 4), Eukaryotic Eukaryotes 28 0.41 Binding ≤ 10μM
HDAC2-1-E Histone Deacetylase 2 (cluster #1 Of 4), Eukaryotic Eukaryotes 21 0.41 Binding ≤ 10μM
HDAC3-1-E Histone Deacetylase 3 (cluster #1 Of 3), Eukaryotic Eukaryotes 20 0.41 Binding ≤ 10μM
HDAC4-1-E Histone Deacetylase 4 (cluster #1 Of 3), Eukaryotic Eukaryotes 5 0.45 Binding ≤ 10μM
HDAC5-1-E Histone Deacetylase 5 (cluster #1 Of 3), Eukaryotic Eukaryotes 9 0.43 Binding ≤ 10μM
HDAC6-1-E Histone Deacetylase 6 (cluster #1 Of 3), Eukaryotic Eukaryotes 300 0.35 Binding ≤ 10μM
HDAC7-1-E Histone Deacetylase 7 (cluster #1 Of 3), Eukaryotic Eukaryotes 70 0.39 Binding ≤ 10μM
HDAC8-1-E Histone Deacetylase 8 (cluster #1 Of 4), Eukaryotic Eukaryotes 136 0.37 Binding ≤ 10μM
HDAC9-1-E Histone Deacetylase 9 (cluster #1 Of 3), Eukaryotic Eukaryotes 11 0.43 Binding ≤ 10μM
CP2D6-1-E Cytochrome P450 2D6 (cluster #1 Of 3), Eukaryotic Eukaryotes 3170 0.30 ADME/T ≤ 10μM
CP3A4-2-E Cytochrome P450 3A4 (cluster #2 Of 4), Eukaryotic Eukaryotes 330 0.35 ADME/T ≤ 10μM
Z80390-1-O PC-3 (Prostate Carcinoma Cells) (cluster #1 Of 10), Other Other 250 0.36 Functional ≤ 10μM
Z80928-3-O HCT-116 (Colon Carcinoma Cells) (cluster #3 Of 9), Other Other 330 0.35 Functional ≤ 10μM
Z81034-6-O A2780 (Ovarian Carcinoma Cells) (cluster #6 Of 10), Other Other 230 0.36 Functional ≤ 10μM
ChEMBL Target Annotations
Uniprot Swissprot Description Affinity (nM) LE (kcal/mol/atom) Type
HDAC1_HUMAN Q13547 Histone Deacetylase 1, Human 19 0.42 Binding ≤ 1μM
HDA10_HUMAN Q969S8 Histone Deacetylase 10, Human 13 0.42 Binding ≤ 1μM
HDA11_HUMAN Q96DB2 Histone Deacetylase 11, Human 11 0.43 Binding ≤ 1μM
HDAC2_HUMAN Q92769 Histone Deacetylase 2, Human 21 0.41 Binding ≤ 1μM
HDAC3_HUMAN O15379 Histone Deacetylase 3, Human 20 0.41 Binding ≤ 1μM
HDAC4_HUMAN P56524 Histone Deacetylase 4, Human 5.3 0.45 Binding ≤ 1μM
HDAC5_HUMAN Q9UQL6 Histone Deacetylase 5, Human 9.2 0.43 Binding ≤ 1μM
HDAC6_HUMAN Q9UBN7 Histone Deacetylase 6, Human 300 0.35 Binding ≤ 1μM
HDAC7_HUMAN Q8WUI4 Histone Deacetylase 7, Human 70 0.39 Binding ≤ 1μM
HDAC8_HUMAN Q9BY41 Histone Deacetylase 8, Human 136 0.37 Binding ≤ 1μM
HDAC9_HUMAN Q9UKV0 Histone Deacetylase 9, Human 11 0.43 Binding ≤ 1μM
HDAC1_HUMAN Q13547 Histone Deacetylase 1, Human 19 0.42 Binding ≤ 10μM
HDA10_HUMAN Q969S8 Histone Deacetylase 10, Human 13 0.42 Binding ≤ 10μM
HDA11_HUMAN Q96DB2 Histone Deacetylase 11, Human 11 0.43 Binding ≤ 10μM
HDAC2_HUMAN Q92769 Histone Deacetylase 2, Human 21 0.41 Binding ≤ 10μM
HDAC3_HUMAN O15379 Histone Deacetylase 3, Human 20 0.41 Binding ≤ 10μM
HDAC4_HUMAN P56524 Histone Deacetylase 4, Human 5.3 0.45 Binding ≤ 10μM
HDAC5_HUMAN Q9UQL6 Histone Deacetylase 5, Human 9.2 0.43 Binding ≤ 10μM
HDAC6_HUMAN Q9UBN7 Histone Deacetylase 6, Human 300 0.35 Binding ≤ 10μM
HDAC7_HUMAN Q8WUI4 Histone Deacetylase 7, Human 70 0.39 Binding ≤ 10μM
HDAC8_HUMAN Q9BY41 Histone Deacetylase 8, Human 136 0.37 Binding ≤ 10μM
HDAC9_HUMAN Q9UKV0 Histone Deacetylase 9, Human 11 0.43 Binding ≤ 10μM
Z81034 Z81034 A2780 (Ovarian Carcinoma Cells) 230 0.36 Functional ≤ 10μM
Z80928 Z80928 HCT-116 (Colon Carcinoma Cells) 330 0.35 Functional ≤ 10μM
Z80390 Z80390 PC-3 (Prostate Carcinoma Cells) 250 0.36 Functional ≤ 10μM
CP2D6_HUMAN P10635 Cytochrome P450 2D6, Human 3170 0.30 ADME/T ≤ 10μM
CP3A4_HUMAN P08684 Cytochrome P450 3A4, Human 330 0.35 ADME/T ≤ 10μM

Reactome Annotations from Targets (via Uniprot)

Description Species
Aflatoxin activation and detoxification
BMAL1:CLOCK,NPAS2 activates circadian gene expression
Circadian Clock
Constitutive Signaling by NOTCH1 HD+PEST Domain Mutants
Constitutive Signaling by NOTCH1 PEST Domain Mutants
CYP2E1 reactions
deactivation of the beta-catenin transactivating complex
Downregulation of SMAD2/3:SMAD4 transcriptional activity
Factors involved in megakaryocyte development and platelet production
Fatty acids
formation of the beta-catenin:TCF transactivating complex
G0 and Early G1
HDACs deacetylate histones
HSF1 activation
Miscellaneous substrates
NoRC negatively regulates rRNA expression
NOTCH1 Intracellular Domain Regulates Transcription
p75NTR negatively regulates cell cycle via SC1
PPARA activates gene expression
Regulation of lipid metabolism by Peroxisome proliferator-activated receptor alp
repression of WNT target genes
REV-ERBA represses gene expression
RNA Polymerase I Transcription Initiation
RORA activates circadian gene expression
SMAD2/SMAD3:SMAD4 heterotrimer regulates transcription
Transcriptional activation of mitochondrial biogenesis
Transcriptional regulation of white adipocyte differentiation
Xenobiotics

Analogs ( Draw Identity 99% 90% 80% 70% )