Structure of PDB 5a3n Chain A

Receptor sequence
>5a3nA (length=456) Species: 9606 (Homo sapiens) [Search protein sequence]
SMFLPPPECPVFEPSWEEFADPFAFIHKIRPIAEQTGICKVRPPPDWQPP
FACDVDKLHFTPRIQRLNELEAQTRVKRDYTLRTFGEMADAFKSDYFNMP
VHMVPTELVEKEFWRLVSTIEEDVTVEYGADIASKEFGSGFPVRDGKIKL
SPEEEEYLDSGWNLNNMPVMEQSVLAHITADICGMKLPWLYVGMCFSSFC
WHIEDHWSYSINYLHWGEPKTWYGVPGYAAEQLENVMKKLAPELFVSQPD
LLHQLVTIMNPNTLMTHEVPVYRTNQCAGEFVITFPRAYHSGFNQGFNFA
EAVNFCTVDWLPLGRQCVEHYRLLHRYCVFSHDEMICKMASKADVLDVVV
ASTVQKDMAIMIEDEKALRETVRKLGVIDSERMDFELLPDDERQCVKCKT
TCFMSAISCSCKPGLLVCLHHVKELCSCPPYKYKLRYRYTLDDLYPMMNA
LKLRAE
3D structure
PDB5a3n Potent and Selective KDM5 Inhibitor Stops Cellular Demethylation of H3K4me3 at Transcription Start Sites and Proliferation of MM1S Myeloma Cells.
ChainA
Resolution2.0 Å
3D
structure
Catalytic site residues are labeled in the structure
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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.
Interaction with ligand
Site
#		 Ligand Ligand
chain		 Binding residues on receptor
(original residue number in PDB)		 Binding residues on receptor
(residue number reindexed from 1)		 Binding affinity
BS01 ZN A C692 C695 C715 H718 C395 C398 C418 H421
BS02 ZN A C706 C708 C723 C725 C409 C411 C426 C428
BS03 MN A L90 N91 L413 T416 E419 L67 N68 L116 T119 E122
BS04 MN A H499 E501 H587 H202 E204 H290
BS05 LQT A Y425 W486 Y488 F496 H499 E501 K517 W519 H587 V600 N601 Y128 W189 Y191 F199 H202 E204 K220 W222 H290 V303 N304 MOAD: ic50=19nM
PDBbind-CN: -logKd/Ki=7.72,IC50=19nM
BindingDB: IC50=19nM
External links
PDB RCSB:5a3n, PDBe:5a3n, PDBj:5a3n
PDBsum5a3n
PubMed28262558
UniProtQ9UGL1|KDM5B_HUMAN Lysine-specific demethylase 5B (Gene Name=KDM5B)

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