Structure of PDB 5fyb Chain A Binding Site BS05

Receptor Information
>5fyb Chain A (length=455) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
SMFLPPPECPVFEPSWEEFADPFAFIHKIRPIAEQTGICKVRPPPDWQPP
FACDVDKLHFTPRIQRLNELEAQTRVKLRDYTLRTFGEMADAFKSDYFNM
PVHMVPTELVEKEFWRLVSTIEEDVTVEYGADIASKEFGSGFPVRDIKLS
PEEEEYLDSGWNLNNMPVMEQSVLAHITADICGMKLPWLYVGMCFSSFCW
HIEDHWSYSINYLHWGEPKTWYGVPGYAAEQLENVMKKLAPELFVSQPDL
LHQLVTIMNPNTLMTHEVPVYRTNQCAGEFVITFPRAYHSGFNQGFNFAE
AVNFCTVDWLPLGRQCVEHYRLLHRYCVFSHDEMICKMASKADVLDVVVA
STVQKDMAIMIEDEKALRETVRKLGVIDSERMDFELLPDDERQCVKCKTT
CFMSAISCSCKPGLLVCLHHVKELCSCPPYKYKLRYRYTLDDLYPMMNAL
KLRAE
Ligand information
Ligand ID77J
InChIInChI=1S/C13H13N3O3S/c17-11(16-19)6-7-20-13-14-10(8-12(18)15-13)9-4-2-1-3-5-9/h1-5,8,19H,6-7H2,(H,16,17)(H,14,15,18)
InChIKeyWNPFBIDOQFZHQF-UHFFFAOYSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.7.6c1ccc(cc1)C2=CC(=O)NC(=N2)SCCC(=O)NO
ACDLabs 12.01C=1(NC(=O)C=C(N=1)c2ccccc2)SCCC(NO)=O
CACTVS 3.385ONC(=O)CCSC1=NC(=CC(=O)N1)c2ccccc2
FormulaC13 H13 N3 O3 S
NameN-hydroxy-3-[(6-oxo-4-phenyl-1,6-dihydropyrimidin-2-yl)sulfanyl]propanamide
ChEMBLCHEMBL413733
DrugBank
ZINCZINC000035050427
PDB chain5fyb Chain A Residue 1761 [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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PDB5fyb Crystal Structure of the Catalytic Domain of Human Jarid1B in Complex with Mc1648
Resolution1.87 Å
Binding residue
(original residue number in PDB)		Y488 F496 H499 E501 S507 N509 K517 H587
Binding residue
(residue number reindexed from 1)		Y190 F198 H201 E203 S209 N211 K219 H289
Annotation score1
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:5fyb, PDBe:5fyb, PDBj:5fyb
PDBsum5fyb
PubMed
UniProtQ9UGL1|KDM5B_HUMAN Lysine-specific demethylase 5B (Gene Name=KDM5B)

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