Structure of PDB 5v9t Chain B

Receptor sequence

>5v9tB (length=593) Species: 9606 (Homo sapiens)

EFVPPPECPVFEPSWEEFTDPLSFIGRIRPLAEKTGICKIRPPKDWQPPF
ACEVKSFRFTPRVQRLNELEAMTRVRLDFLDQLAKFWELQGSTLKIPVVE
RKILDLYALSKIVASKGGFEMVTKEKKWSKVGSRLGYLPGKGTGSLLKSH
YERILYPYELFQSGVSLMGVQMEVLSTDTQTSPEPGTRYTLQSFGEMADN
FKSDYFNMPVHMVPTELVEKEFWRLVSSIEEDVIVEYGADISSKDFGSGF
PVKDGRRKILPEEEEYALSGWNLNNMPVLEQSVLAHINVDISGMKVPWLY
VGMCFSSFCWHIEDHWSYSINYLHWGEPKTWYGVPSHAAEQLEEVMRELA
PELFESQPDLLHQLVTIMNPNVLMEHGVPVYRTNQCAGEFVVTFPRAYHS
GFNQGYNFAEAVNFCTADWLPIGRQCVNHYRRLRRHCVFSHEELIFKMAA
DPECLDVGLAAMVCKELTLMTEEETRLRESVVQMGVLMSEEEVFELVPDD
ERQCSACRTTCFLSALTCSCNPERLVCLYHPTDLCPCPMQKKCLRYRYPL
EDLPSLLYGVKVRAQSYDTWVSVMLEDAEDRKYPENDLFRKLR

3D structure

• PDB: 5v9t From a novel HTS hit to potent, selective, and orally bioavailable KDM5 inhibitors.
• Chain: B
• Resolution: 3.05 Å

Enzymatic activity

• Catalytic site (original residue number in PDB): G465 Y472 H483 E485 H571 A583
• Catalytic site (residue number reindexed from 1): G293 Y300 H311 E313 H399 A411
• 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	E663 E664	E491 E492
BS02	ZN	B	C676 C679 C699	C504 C507 C527
BS03	ZN	B	C690 C692 C709	C518 C520 C537
BS04	90V	B	Y472 F480 H483 E485 S491 N493 K501 H571 N575 V584 N585	Y300 F308 H311 E313 S319 N321 K329 H399 N403 V412 N413	BindingDB: IC50=570nM,Kd=2400nM,EC50=960nM

Gene Ontology

Molecular Function

• GO:0003677 DNA binding

External links

• PDB: RCSB:5v9t, PDBe:5v9t, PDBj:5v9t
• PDBsum: 5v9t
• PubMed: 28512031
• UniProt: P29375|KDM5A_HUMAN Lysine-specific demethylase 5A (Gene Name=KDM5A)