Structure of PDB 6dq4 Chain A Binding Site BS01

Receptor Information
>6dq4 Chain A (length=312) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
AEFVPPPECPVFEPSWEEFTDPLSFIGRIRPLAEKTGICKIRPPKDWQPP
FACEVKSFRFTPRVQRLNELEAMTRPREAFGFEQAVREYTLQSFGEMADN
FKSDYFNMPVHMVPTELVEKEFWRLVSSIEEDVIVEYGADISSKDFGSGF
PVKDGRRKILPEEEEYALSGWNLNNMPVLEQSVLAHINVMKVPWLYVGMC
FSSFCWHIEDHWSYSINYLHWGEPKTWYGVPSHAAEQLEEVMRELAPELF
ESQPDLLHQLVTIMNPNVLMEHGVPVYRTNQCAGEFVVTFPRAYHSGFNQ
GYNFAEAVNFCT
Ligand information
Ligand IDK0I
InChIInChI=1S/C22H23N5O2/c28-21(29)8-12-24-19-15-20(26-22(25-19)18-7-3-4-11-23-18)27-13-9-16-5-1-2-6-17(16)10-14-27/h1-7,11,15H,8-10,12-14H2,(H,28,29)(H,24,25,26)
InChIKeyAVZCPICCWKMZDT-UHFFFAOYSA-N
SMILES
SoftwareSMILES
CACTVS 3.385OC(=O)CCNc1cc(nc(n1)c2ccccn2)N3CCc4ccccc4CC3
OpenEye OEToolkits 1.7.6c1ccc2c(c1)CCN(CC2)c3cc(nc(n3)c4ccccn4)NCCC(=O)O
ACDLabs 12.01O=C(O)CCNc2nc(c1ncccc1)nc(c2)N3CCc4c(CC3)cccc4
FormulaC22 H23 N5 O2
Name3-[[2-pyridin-2-yl-6-(1,2,4,5-tetrahydro-3-benzazepin-3-yl)pyrimidin-4-yl]amino]propanoic acid;
3-((6-(4,5-dihydro-1H-benzo[d]azepin-3(2H)-yl)-2-(pyridin-2-yl)pyrimidin-4-yl)amino)propanoic acid
ChEMBLCHEMBL3188597
DrugBank
ZINCZINC000095616592
PDB chain6dq4 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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PDB6dq4 Structure-Based Engineering of Irreversible Inhibitors against Histone Lysine Demethylase KDM5A.
Resolution1.392 Å
Binding residue
(original residue number in PDB)		R73 Y409 A411 D412 Y472 F480 H483 E485 K501
Binding residue
(residue number reindexed from 1)		R63 Y137 A139 D140 Y196 F204 H207 E209 K225
Annotation score1
Binding affinityMOAD: Kd=12uM
PDBbind-CN: -logKd/Ki=4.92,Kd=12uM
BindingDB: IC50=110000nM,Kd=12000nM
Enzymatic activity
Catalytic site (original residue number in PDB) Y472 H483 E485 H571 A583
Catalytic site (residue number reindexed from 1) Y196 H207 E209 H295 A307
Enzyme Commision number 1.14.11.67: [histone H3]-trimethyl-L-lysine(4) demethylase.
External links
PDB RCSB:6dq4, PDBe:6dq4, PDBj:6dq4
PDBsum6dq4
PubMed30392349
UniProtP29375|KDM5A_HUMAN Lysine-specific demethylase 5A (Gene Name=KDM5A)

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