Structure of PDB 5fyu Chain A Binding Site BS03

Receptor Information

>5fyu Chain A (length=457) Species: 9606 (Homo sapiens)

SMFLPPPECPVFEPSWEEFADPFAFIHKIRPIAEQTGICKVRPPPDWQPP
FACDVDKLHFTPRIQRLNELEAQTRVKLRDYTLRTFGEMADAFKSDYFNM
PVHMVPTELVEKEFWRLVSTIEEDVTVEYGADIASKEFGSGFPVRDGIKL
SPEEEEYLDSGWNLNNMPVMEQSVLAHITADICGMKLPWLYVGMCFSSFC
WHIEDHWSYSINYLHWGEPKTWYGVPGYAAEQLENVMKKLAPELFVSQPD
LLHQLVTIMNPNTLMTHEVPVYRTNQCAGEFVITFPRAYHSGFNQGFNFA
EAVNFCTVDWLPLGRQCVEHYRLLHRYCVFSHDEMICKMASKADVLDVVV
ASTVQKDMAIMIEDEKALRETVRKLGVIDSERMDFELLPDDERQCVKCKT
TCFMSAISCSCKPGLLVCLHHVKELCSCPPYKYKLRYRYTLDDLYPMMNA
LKLRAES

Ligand information

• Ligand ID: BY4
• InChI: InChI=1S/C9H10N2O/c1-5-3-2-4-6-7(5)8(10)9(12)11-6/h2-4,8H,10H2,1H3,(H,11,12)/t8-/m1/s1
• InChIKey: DXMQUOQQGLIRSR-MRVPVSSYSA-N
• SMILES:
  CACTVS 3.385: Cc1cccc2NC(=O)[CH](N)c12
  OpenEye OEToolkits 1.7.6: Cc1cccc2c1[C@H](C(=O)N2)N
  CACTVS 3.385: Cc1cccc2NC(=O)[C@H](N)c12
  OpenEye OEToolkits 1.7.6: Cc1cccc2c1C(C(=O)N2)N
• Formula: C9 H10 N2 O
• Name: (3R)-3-azanyl-4-methyl-1,3-dihydroindol-2-one
• ZINC: ZINC000100287409
• PDB chain: 5fyu Chain A Residue 1774

Receptor-Ligand Complex Structure

Structure summary

• PDB: 5fyu Crystal Structure of the Catalytic Domain of Human Jarid1B in Complex with N10042A
• Resolution: 2.06 Å
• Binding residue (original residue number in PDB): Y425 Y488 F496 K517
• Binding residue (residue number reindexed from 1): Y129 Y191 F199 K220
• Annotation score: 1

Enzymatic activity

• Catalytic site (original residue number in PDB): G481 Y488 H499 E501 H587 A599
• Catalytic site (residue number reindexed from 1): G184 Y191 H202 E204 H290 A302
• Enzyme Commision number: 1.14.11.67: [histone H3]-trimethyl-L-lysine(4) demethylase.

External links

• PDB: RCSB:5fyu, PDBe:5fyu, PDBj:5fyu
• PDBsum: 5fyu
• UniProt: Q9UGL1|KDM5B_HUMAN Lysine-specific demethylase 5B (Gene Name=KDM5B)