Structure of PDB 6bgz Chain A Binding Site BS01

Receptor Information
>6bgz Chain A (length=293) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
AEFVPPPECPVFEPSWEEFTDPLSFIGRIRPLAEKTGICKIRPPKDWQPP
FACEVKSFRFTPRVQRLNELEAMAVREYTLQSFGEMADNFKSDYFNMPVH
MVPTELVEKEFWRLVSSIEEDVIVEYGADISSKDFGSGFPVKDGRRKILP
EEEEYALSGWNLNNMPVLEQSKVPWLYVGMCFSSFCWHIEDHWSYSINYL
HWGEPKTWYGVPSHAAEQLEEVMRELAPELFESQPDLLHQLVTIMNPNVL
MEHGVPVYRTNQCAGEFVVTFPRAYHSGFNQGYNFAEAVNFCT
Ligand information
Ligand IDDNV
InChIInChI=1S/C21H19ClN4O3/c1-26-10-9-24-18(26)7-11-29-20(13-4-2-3-5-15(13)22)17-12-16-19(25-17)14(21(27)28)6-8-23-16/h2-6,8-10,12,20,25H,7,11H2,1H3,(H,27,28)/t20-/m0/s1
InChIKeyULBCSYUKODTPKF-FQEVSTJZSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 2.0.6Cn1ccnc1CCOC(c2ccccc2Cl)c3cc4c([nH]3)c(ccn4)C(=O)O
ACDLabs 12.01C(OC(c1c(cccc1)Cl)c2cc3c(n2)c(C(=O)O)ccn3)Cc4nccn4C
CACTVS 3.385Cn1ccnc1CCO[C@H](c2[nH]c3c(c2)nccc3C(O)=O)c4ccccc4Cl
OpenEye OEToolkits 2.0.6Cn1ccnc1CCO[C@@H](c2ccccc2Cl)c3cc4c([nH]3)c(ccn4)C(=O)O
CACTVS 3.385Cn1ccnc1CCO[CH](c2[nH]c3c(c2)nccc3C(O)=O)c4ccccc4Cl
FormulaC21 H19 Cl N4 O3
Name2-{(S)-(2-chlorophenyl)[2-(1-methyl-1H-imidazol-2-yl)ethoxy]methyl}-1H-pyrrolo[3,2-b]pyridine-7-carboxylic acid
ChEMBL
DrugBank
ZINC
PDB chain6bgz Chain A Residue 601 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
PDB6bgz Insights into the Action of Inhibitor Enantiomers against Histone Lysine Demethylase 5A.
Resolution1.688 Å
Binding residue
(original residue number in PDB)		Y409 Y472 F480 C481 H483 K501 W503 Q535 L536 H571
Binding residue
(residue number reindexed from 1)		Y126 Y177 F185 C186 H188 K206 W208 Q240 L241 H276
Annotation score1
Binding affinityMOAD: Kd=0.41uM
PDBbind-CN: -logKd/Ki=6.39,Kd=0.41uM
BindingDB: Kd=410nM,IC50=1400nM
Enzymatic activity
Catalytic site (original residue number in PDB) Y472 H483 E485 H571 A583
Catalytic site (residue number reindexed from 1) Y177 H188 E190 H276 A288
Enzyme Commision number 1.14.11.67: [histone H3]-trimethyl-L-lysine(4) demethylase.
External links
PDB RCSB:6bgz, PDBe:6bgz, PDBj:6bgz
PDBsum6bgz
PubMed29537847
UniProtP29375|KDM5A_HUMAN Lysine-specific demethylase 5A (Gene Name=KDM5A)

[Back to BioLiP]