Structure of PDB 5lw9 Chain A Binding Site BS03

Receptor Information
>5lw9 Chain A (length=456) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MFLPPPECPVFEPSWEEFADPFAFIHKIRPIAEQTGICKVRPPPDWQPPF
ACDVDKLHFTPRIQRLNELEAQTRVKARDYTLRTFGEMADAFKSDYFNMP
VHMVPTELVEKEFWRLVSTIEEDVTVEYGADIASKEFGSGFPVRDGIKLS
PEEEEYLDSGWNLNNMPVMEQSVLAHITADICGMKLPWLYVGMCFSSFCW
HIEDHWSYSINYLHWGEPKTWYGVPGYAAEQLENVMKKLAPELFVSQPDL
LHQLVTIMNPNTLMTHEVPVYRTNQCAGEFVITFPRAYHSGFNQGFNFAE
AVNFCTVDWLPLGRQCVEHYRLLHRYCVFSHDEMICKMASKADVLDVVVA
STVQKDMAIMIEDEKALRETVRKLGVIDSERMDFELLPDDERQCVKCKTT
CFMSAISCSCKPGLLVCLHHVKELCSCPPYKYKLRYRYTLDDLYPMMNAL
KLRAES
Ligand information
Ligand ID5UJ
InChIInChI=1S/C23H22Cl2N6O/c24-18-9-17(10-19(25)11-18)16-3-7-30(8-4-16)6-2-15-12-29-31(13-15)22-21-20(1-5-26-22)23(32)28-14-27-21/h1,5,9-14,16H,2-4,6-8H2,(H,27,28,32)
InChIKeyRLRGPZGIQMEBLC-UHFFFAOYSA-N
SMILES
SoftwareSMILES
CACTVS 3.385Clc1cc(Cl)cc(c1)C2CCN(CC2)CCc3cnn(c3)c4nccc5C(=O)NC=Nc45
OpenEye OEToolkits 2.0.4c1cnc(c2c1C(=O)NC=N2)n3cc(cn3)CCN4CCC(CC4)c5cc(cc(c5)Cl)Cl
FormulaC23 H22 Cl2 N6 O
Name8-[4-[2-[4-[3,5-bis(chloranyl)phenyl]piperidin-1-yl]ethyl]pyrazol-1-yl]-3~{H}-pyrido[3,4-d]pyrimidin-4-one
ChEMBLCHEMBL3775894
DrugBank
ZINCZINC000263620975
PDB chain5lw9 Chain A Residue 808 [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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PDB5lw9 Crystal structure of human JARID1B in complex with S40563a
Resolution2.3 Å
Binding residue
(original residue number in PDB)		Y425 D428 W486 Y488 F496 H499 E501 K517 W519 H587
Binding residue
(residue number reindexed from 1)		Y128 D131 W188 Y190 F198 H201 E203 K219 W221 H289
Annotation score1
Binding affinityBindingDB: IC50=14nM
Enzymatic activity
Catalytic site (original residue number in PDB) G481 Y488 H499 E501 H587 A599
Catalytic site (residue number reindexed from 1) G183 Y190 H201 E203 H289 A301
Enzyme Commision number 1.14.11.67: [histone H3]-trimethyl-L-lysine(4) demethylase.
External links
PDB RCSB:5lw9, PDBe:5lw9, PDBj:5lw9
PDBsum5lw9
PubMed
UniProtQ9UGL1|KDM5B_HUMAN Lysine-specific demethylase 5B (Gene Name=KDM5B)

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