Structure of PDB 5k4l Chain B

Receptor sequence
>5k4lB (length=577) Species: 9606 (Homo sapiens) [Search protein sequence]
EFVPPPECPVFEPSWEEFTDPLSFIGRIRPLAEKTGICKIRPPKDWQPPF
ACEVKSFRFTPRVQRLNELEAMTRVRLDFLDQLAKFWELQGSTLKIPVVE
RKILDLYALSKIVASKGGFEMVTKEKKWSKVGSRLGYLPGKGTGSLLKSH
YERILYPYELFQSGVSLMGVQMYTLQSFGEMADNFKSDYFNMPVHMVPTE
LVEKEFWRLVSSIEEDVIVEYGADISSKDFGSGFPVKDGRRKILPEEEEY
ALSGWNLNNMPVLEQSVLAHINVDISGMKVPWLYVGMCFSSFCWHIEDHW
SYSINYLHWGEPKTWYGVPSHAAEQLEEVMRELAPELFESQPDLLHQLVT
IMNPNVLMEHGVPVYRTNQCAGEFVVTFPRAYHSGFNQGYNFAEAVNFCT
ADWLPIGRQCVNHYRRLRRHCVFSHEELIFKMAADPECLDVGLAAMVCKE
LTLMTEEETRLRESVVQMGVLMSEEEVFELVPDDERQCSACRTTCFLSAL
TCSCNPERLVCLYHPTDLCPCPMQKKCLRYRYPLEDLPSLLYGVKVRAQS
YDTWVSVMLEDAEDRKYPENDLFRKLR
3D structure
PDB5k4l Design and evaluation of 1,7-naphthyridones as novel KDM5 inhibitors.
ChainB
Resolution3.179 Å
3D
structure
Catalytic site residues are labeled in the structure
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Enzymatic activity
Catalytic site (original residue number in PDB) G465 Y472 H483 E485 H571 A583
Catalytic site (residue number reindexed from 1) G277 Y284 H295 E297 H383 A395
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 peptide B E662 E663 E664 E673 E695 R717 E474 E475 E476 E485 E507 R529
BS02 ZN B C679 H702 C491 H514
BS03 ZN B C690 C707 C709 C502 C519 C521
BS04 6QN B Y472 F480 H483 N493 K501 W503 H571 Y284 F292 H295 N305 K313 W315 H383 BindingDB: IC50=50nM
Gene Ontology

View graph for
Molecular Function
External links
PDB RCSB:5k4l, PDBe:5k4l, PDBj:5k4l
PDBsum5k4l
PubMed27499454
UniProtP29375|KDM5A_HUMAN Lysine-specific demethylase 5A (Gene Name=KDM5A)

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