Structure of PDB 6dq8 Chain A Binding Site BS01

Receptor Information
>6dq8 Chain A (length=302) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
AEFVPPPECPVFEPSWEEFTDPLSFIGRIRPLAEKTGICKIRPPKDWQPP
FACEVKSFRFTPRVQRLNELEAMTAFGFEQAVREYTLQSFGEMADNFKSD
YFNMPVHMVPTELVEKEFWRLVSSIEEDVIVEYGADISSKDFGSGFPVKD
GRRKILPEEEEYALSGWNLNNMPVLEQSVLKVPWLYVGMCFSSFCWHIED
HWSYSINYLHWGEPKTWYGVPSHAAEQLEEVMRELAPELFESQPDLLHQL
VTIMNPNVLMEHGVPVYRTNQCAGEFVVTFPRAYHSGFNQGYNFAEAVNF
CT
Ligand information
Ligand IDH6S
InChIInChI=1S/C22H23ClN2O3S/c1-25-11-4-5-14(25)9-12-28-20(15-6-2-3-7-17(15)23)19-13-18-21(29-19)16(22(26)27)8-10-24-18/h2-3,6-8,10,13-14,20H,4-5,9,11-12H2,1H3,(H,26,27)/t14-,20+/m0/s1
InChIKeyCKHGFLIUOABPPV-VBKZILBWSA-N
SMILES
SoftwareSMILES
CACTVS 3.385CN1CCC[CH]1CCO[CH](c2sc3c(c2)nccc3C(O)=O)c4ccccc4Cl
ACDLabs 12.01c1(ccccc1C(OCCC2CCCN2C)c3sc4c(c3)nccc4C(=O)O)Cl
OpenEye OEToolkits 2.0.6CN1CCC[C@H]1CCO[C@H](c2ccccc2Cl)c3cc4c(s3)c(ccn4)C(=O)O
CACTVS 3.385CN1CCC[C@H]1CCO[C@@H](c2sc3c(c2)nccc3C(O)=O)c4ccccc4Cl
OpenEye OEToolkits 2.0.6CN1CCCC1CCOC(c2ccccc2Cl)c3cc4c(s3)c(ccn4)C(=O)O
FormulaC22 H23 Cl N2 O3 S
Name2-[(R)-(2-chlorophenyl){2-[(2S)-1-methylpyrrolidin-2-yl]ethoxy}methyl]thieno[3,2-b]pyridine-7-carboxylic acid
ChEMBL
DrugBank
ZINC
PDB chain6dq8 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

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PDB6dq8 Structure-Based Engineering of Irreversible Inhibitors against Histone Lysine Demethylase KDM5A.
Resolution1.46 Å
Binding residue
(original residue number in PDB)		Y409 A411 W470 Y472 F480 C481 H483 K501 W503 H571
Binding residue
(residue number reindexed from 1)		Y133 A135 W184 Y186 F194 C195 H197 K215 W217 H285
Annotation score1
Binding affinityMOAD: Kd=0.26uM
PDBbind-CN: -logKd/Ki=6.59,Kd=0.26uM
BindingDB: Kd=260nM,IC50=320nM
Enzymatic activity
Catalytic site (original residue number in PDB) Y472 H483 E485 H571 A583
Catalytic site (residue number reindexed from 1) Y186 H197 E199 H285 A297
Enzyme Commision number 1.14.11.67: [histone H3]-trimethyl-L-lysine(4) demethylase.
External links
PDB RCSB:6dq8, PDBe:6dq8, PDBj:6dq8
PDBsum6dq8
PubMed30392349
UniProtP29375|KDM5A_HUMAN Lysine-specific demethylase 5A (Gene Name=KDM5A)

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