Structure of PDB 6ej0 Chain A Binding Site BS04

Receptor Information

>6ej0 Chain A (length=453) Species: 9606 (Homo sapiens)

MFLPPPECPVFEPSWEEFADPFAFIHKIRPIAEQTGICKVRPPPDWQPPF
ACDVDKLHFTPRIQRLNELEAQTRRDYTLRTFGEMADAFKSDYFNMPVHM
VPTELVEKEFWRLVSTIEEDVTVEYGADIASKEFGSGFPVRDGIKLSPEE
EEYLDSGWNLNNMPVMEQSVLAHITADICGMKLPWLYVGMCFSSFCWHIE
DHWSYSINYLHWGEPKTWYGVPGYAAEQLENVMKKLAPELFVSQPDLLHQ
LVTIMNPNTLMTHEVPVYRTNQCAGEFVITFPRAYHSGFNQGFNFAEAVN
FCTVDWLPLGRQCVEHYRLLHRYCVFSHDEMICKMASKADVLDVVVASTV
QKDMAIMIEDEKALRETVRKLGVIDSERMDFELLPDDERQCVKCKTTCFM
SAISCSCKPGLLVCLHHVKELCSCPPYKYKLRYRYTLDDLYPMMNALKLR
AES

Ligand information

• Ligand ID: B7K
• InChI: InChI=1S/C21H23N7O2/c1-4-17(29)26-7-5-16(6-8-26)27-12-15(11-23-27)19-18(13(2)3)21(30)28-20(25-19)14(9-22)10-24-28/h4,10-13,16,18H,1,5-8H2,2-3H3/t18-/m0/s1
• InChIKey: KGLWYCXNVRPKIE-SFHVURJKSA-N
• SMILES:
  OpenEye OEToolkits 2.0.6: CC(C)C1C(=Nc2c(cnn2C1=O)C#N)c3cnn(c3)C4CCN(CC4)C(=O)C=C
  CACTVS 3.385: CC(C)[CH]1C(=O)n2ncc(C#N)c2N=C1c3cnn(c3)C4CCN(CC4)C(=O)C=C
  CACTVS 3.385: CC(C)[C@@H]1C(=O)n2ncc(C#N)c2N=C1c3cnn(c3)C4CCN(CC4)C(=O)C=C
• Formula: C21 H23 N7 O2
• Name: 7-oxidanylidene-6-propan-2-yl-5-[1-(1-prop-2-enoylpiperidin-4-yl)pyrazol-4-yl]-6~{H}-pyrazolo[1,5-a]pyrimidine-3-carbonitrile
• PDB chain: 6ej0 Chain A Residue 811

Receptor-Ligand Complex Structure

Structure summary

• PDB: 6ej0 Crystal structure of KDM5B in complex with KDOPZ000049a.
• Resolution: 2.06 Å
• Binding residue (original residue number in PDB): R86 R98 Y425 W486 Y488 S495 F496 H499 K517 H587
• Binding residue (residue number reindexed from 1): R62 R74 Y125 W185 Y187 S194 F195 H198 K216 H286
• Annotation score: 1

Enzymatic activity

• Enzyme Commision number: 1.14.11.67: [histone H3]-trimethyl-L-lysine(4) demethylase.

External links

• PDB: RCSB:6ej0, PDBe:6ej0, PDBj:6ej0
• PDBsum: 6ej0
• UniProt: Q9UGL1|KDM5B_HUMAN Lysine-specific demethylase 5B (Gene Name=KDM5B)