Structure of PDB 2p5b Chain A Binding Site BS04

Receptor Information
>2p5b Chain A (length=347) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
ASESETLNPSARIMTFYPTMEEFRNFSRYIAYIESQGAHRAGLAKVVPPK
EWKPRASYDDIDDLVIPAPIQQLVTGQSGLFTQYNIQKKAMTVREFRKIA
NSDKYCTPRYSEFEELERKYWKNLTFNPPIYGADVNGTLYEKHVDEWNIG
RLRTILDLVEKESGITIEGVNTPYLYFGMWKTSFAWHTEDMDLYSINYLH
FGEPKSWYSVPPEHGKRLERLAKGFFPGSAQSCEAFLRHKMTLISPLMLK
KYGIPFDKVTQEAGEFMITFPYGYHAGFNHGFNCAESTNFATRRWIEYGK
QAVLCSCRKDMVKISMDVFVRKFQPERYKLWKAGKDNTVIDHTLPTP
Ligand information
Ligand IDOGA
InChIInChI=1S/C4H5NO5/c6-2(7)1-5-3(8)4(9)10/h1H2,(H,5,8)(H,6,7)(H,9,10)
InChIKeyBIMZLRFONYSTPT-UHFFFAOYSA-N
SMILES
SoftwareSMILES
CACTVS 3.341OC(=O)CNC(=O)C(O)=O
ACDLabs 10.04O=C(O)C(=O)NCC(=O)O
OpenEye OEToolkits 1.5.0C(C(=O)O)NC(=O)C(=O)O
FormulaC4 H5 N O5
NameN-OXALYLGLYCINE
ChEMBLCHEMBL90852
DrugBank
ZINCZINC000001534133
PDB chain2p5b Chain A Residue 401 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
PDB2p5b Structural basis of the recognition of a methylated histone tail by JMJD2A.
Resolution1.99 Å
Binding residue
(original residue number in PDB)		Y132 F185 H188 E190 S196 N198 W208 H276
Binding residue
(residue number reindexed from 1)		Y131 F184 H187 E189 S195 N197 W207 H275
Annotation score2
Binding affinityBindingDB: IC50=250000nM
Enzymatic activity
Catalytic site (original residue number in PDB) G170 Y177 H188 E190 H276 S288
Catalytic site (residue number reindexed from 1) G169 Y176 H187 E189 H275 S287
Enzyme Commision number 1.14.11.66: [histone H3]-trimethyl-L-lysine(9) demethylase.
1.14.11.69: [histone H3]-trimethyl-L-lysine(36) demethylase.
External links
PDB RCSB:2p5b, PDBe:2p5b, PDBj:2p5b
PDBsum2p5b
PubMed17567753
UniProtO75164|KDM4A_HUMAN Lysine-specific demethylase 4A (Gene Name=KDM4A)

[Back to BioLiP]