Structure of PDB 6g5x Chain B Binding Site BS02

Receptor Information
>6g5x Chain B (length=344) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
SARIMTFYPTMEEFRNFSRYIAYIESQGAHRAGLAKVVPPKEWKPRASYD
DIDDLVIPAPIQQLVTGQSGLFTQYNIQKKAMTVREFRKIANSDKYCTPR
YSEFEELERKYWKNLTFNPPIYGADVNGTLYEKHVDEWNIGRLRTILDLV
EKESGITIEGVNTPYLYFGMWKTSFAWHTEDMDLYSINYLHFGEPKSWYS
VPPEHGKRLERLAKGFFPGSAQSCEAFLRHKMTLISPLMLKKYGIPFDKV
TQEAGEFMITFPYGYHAGFNHGFNCAESTNFATRRWIEYGKQAVLCSCRK
DMVKISMDVFVRKFQPERYKLWKAGKDNTVIDHTLPTPEAAEFL
Ligand information
Ligand IDMY7
InChIInChI=1S/C18H14N4O3/c1-10-15(11-5-3-2-4-6-11)16(23)22(21-10)18-19-13-8-7-12(17(24)25)9-14(13)20-18/h2-9,15H,1H3,(H,19,20)(H,24,25)/t15-/m0/s1
InChIKeyIRYCJDGHIUCPHS-HNNXBMFYSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 2.0.6CC1=NN(C(=O)C1c2ccccc2)c3[nH]c4cc(ccc4n3)C(=O)O
CACTVS 3.385CC1=NN(C(=O)[CH]1c2ccccc2)c3[nH]c4cc(ccc4n3)C(O)=O
CACTVS 3.385CC1=NN(C(=O)[C@@H]1c2ccccc2)c3[nH]c4cc(ccc4n3)C(O)=O
FormulaC18 H14 N4 O3
Name2-(3-methyl-5-oxidanylidene-4-phenyl-4~{H}-pyrazol-1-yl)-3~{H}-benzimidazole-5-carboxylic acid
ChEMBL
DrugBank
ZINC
PDB chain6g5x Chain B Residue 406 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

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PDB6g5x Enhanced Properties of a Benzimidazole Benzylpyrazole Lysine Demethylase Inhibitor: Mechanism-of-Action, Binding Site Analysis, and Activity in Cellular Models of Prostate Cancer.
Resolution1.78 Å
Binding residue
(original residue number in PDB)		F114 E115 E118 S207 Y209 K259 V260 T261
Binding residue
(residue number reindexed from 1)		F104 E105 E108 S197 Y199 K249 V250 T251
Annotation score1
Enzymatic activity
Catalytic site (original residue number in PDB) G170 Y177 H188 E190 H276 S288
Catalytic site (residue number reindexed from 1) G160 Y167 H178 E180 H266 S278
Enzyme Commision number 1.14.11.66: [histone H3]-trimethyl-L-lysine(9) demethylase.
1.14.11.69: [histone H3]-trimethyl-L-lysine(36) demethylase.
External links
PDB RCSB:6g5x, PDBe:6g5x, PDBj:6g5x
PDBsum6g5x
PubMed34555281
UniProtO75164|KDM4A_HUMAN Lysine-specific demethylase 4A (Gene Name=KDM4A)

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