Structure of PDB 6dqb Chain A Binding Site BS03

Receptor Information
>6dqb Chain A (length=295) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
AEFVPPPECPVFEPSWEEFTDPLSFIGRIRPLAEKTGICKIRPPKDWQPP
FACEVKSFRFTPRVQRLNELEAMAVREYTLQSFGEMADNFKSDYFNMPVH
MVPTELVEKEFWRLVSSIEEDVIVEYGADISSKDFGSGFPVKDGRRKILP
EEEEYALSGWNLNNMPVLEQSVLKVPWLYVGMCFSSFCWHIEDHWSYSIN
YLHWGEPKTWYGVPSHAAEQLEEVMRELAPELFESQPDLLHQLVTIMNPN
VLMEHGVPVYRTNQCAGEFVVTFPRAYHSGFNQGYNFAEAVNFCT
Ligand information
Ligand IDHZM
InChIInChI=1S/C28H36N4O4S/c1-31(2)13-7-10-25(33)30-21-9-6-8-20(18-21)26(36-17-16-32-14-4-3-5-15-32)24-19-23-27(37-24)22(28(34)35)11-12-29-23/h6,8-9,11-12,18-19,26H,3-5,7,10,13-17H2,1-2H3,(H,30,33)(H,34,35)/t26-/m0/s1
InChIKeyGTUZDQNWYGEDTB-SANMLTNESA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 2.0.6CN(C)CCCC(=O)Nc1cccc(c1)C(c2cc3c(s2)c(ccn3)C(=O)O)OCCN4CCCCC4
CACTVS 3.385CN(C)CCCC(=O)Nc1cccc(c1)[CH](OCCN2CCCCC2)c3sc4c(c3)nccc4C(O)=O
OpenEye OEToolkits 2.0.6CN(C)CCCC(=O)Nc1cccc(c1)[C@@H](c2cc3c(s2)c(ccn3)C(=O)O)OCCN4CCCCC4
CACTVS 3.385CN(C)CCCC(=O)Nc1cccc(c1)[C@H](OCCN2CCCCC2)c3sc4c(c3)nccc4C(O)=O
ACDLabs 12.01C(=O)(O)c2c1sc(cc1ncc2)C(c3cc(ccc3)NC(CCCN(C)C)=O)OCCN4CCCCC4
FormulaC28 H36 N4 O4 S
Name2-{(S)-(3-{[4-(dimethylamino)butanoyl]amino}phenyl)[2-(piperidin-1-yl)ethoxy]methyl}thieno[3,2-b]pyridine-7-carboxylic acid;
2-{(S)-(3-{[(2E)-4-(dimethylamino)but-2-enoyl]amino}phenyl)[2-(piperidin-1-yl)ethoxy]methyl}thieno[3,2-b]pyridine-7-carboxylic acid, bound form
ChEMBL
DrugBank
ZINC
PDB chain6dqb Chain A Residue 603 [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]
PDB6dqb Structure-Based Engineering of Irreversible Inhibitors against Histone Lysine Demethylase KDM5A.
Resolution1.791 Å
Binding residue
(original residue number in PDB)
R73 Y409 A411 D412 Y472 F480 C481 H483 K501 W503 H571
Binding residue
(residue number reindexed from 1)
R63 Y126 A128 D129 Y179 F187 C188 H190 K208 W210 H278
Annotation score1
Binding affinityPDBbind-CN: -logKd/Ki=6.49,IC50=0.32uM
Enzymatic activity
Catalytic site (original residue number in PDB) Y472 H483 E485 H571 A583
Catalytic site (residue number reindexed from 1) Y179 H190 E192 H278 A290
Enzyme Commision number 1.14.11.67: [histone H3]-trimethyl-L-lysine(4) demethylase.
External links
PDB RCSB:6dqb, PDBe:6dqb, PDBj:6dqb
PDBsum6dqb
PubMed30392349
UniProtP29375|KDM5A_HUMAN Lysine-specific demethylase 5A (Gene Name=KDM5A)

[Back to BioLiP]