Structure of PDB 5a2s Chain B Binding Site BS01

Receptor Information

>5a2s Chain B (length=380) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]

TTGLVYDTLMLKHQCTCGSSSSHPEHAGRIQSIWSRLQETGLRGKCECIR
GRKATLEELQTVHSEAHTLLYGTNPANRQKLDSKKLLGSLASVFVRLPCG
GVGVDSDTIWNEVHSAGAARLAVGCVVELVFKVATGELKNGFAVVRPPGH
HAEESTPMGFCYFNSVAVAAKLLQQRLSVSKILIVDWDVHHGNGTQQAFY
SDPSVLYMSLHRYDDGNFFPGSGAPDEVGTGPGVGFNVNMAFTGGLDPPM
GDAEYLAAFRTVVMPIASEFAPDVVLVSSGFDAVEGHPTPLGGYNLSARC
FGYLTKQLMGLAGGRIVLALEGGHDLTAICDASEACVSALLGNELDPLPE
KVLQQRPNANAVRSMEKVMEIHSKYWRCLQ

Ligand information

Ligand ID

OTF

InChI

InChI=1S/C20H15F2N3O2/c21-15-10-23-18(24-11-15)14-8-6-13(7-9-14)17-16(12-4-2-1-3-5-12)20(17,22)19(26)25-27/h1-11,16-17,27H,(H,25,26)/t16-,17-,20+/m1/s1

InChIKey

MREATSZIGJDNKB-HLIPFELVSA-N

SMILES

Software	SMILES
OpenEye OEToolkits 1.7.6	c1ccc(cc1)C2C(C2(C(=O)NO)F)c3ccc(cc3)c4ncc(cn4)F
CACTVS 3.385	ONC(=O)[C]1(F)[CH]([CH]1c2ccc(cc2)c3ncc(F)cn3)c4ccccc4
OpenEye OEToolkits 1.7.6	c1ccc(cc1)[C@@H]2[C@H]([C@@]2(C(=O)NO)F)c3ccc(cc3)c4ncc(cn4)F
CACTVS 3.385	ONC(=O)[C@]1(F)[C@@H]([C@H]1c2ccc(cc2)c3ncc(F)cn3)c4ccccc4

Formula

C20 H15 F2 N3 O2

Name

(1S,2S,3S)-1-fluoranyl-2-[4-(5-fluoranylpyrimidin-2-yl)phenyl]-N-oxidanyl-3-phenyl-cyclopropane-1-carboxamide

PDB chain

5a2s Chain B Residue 1 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]

Receptor-Ligand Complex Structure

Global view

Local view

Structure summary

[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]

PDB	5a2s Potent, Selective, and Cns-Penetrant Tetrasubstituted Cyclopropane Class Iia Histone Deacetylase (Hdac) Inhibitors.
Resolution	2.65 Å
Binding residue (original residue number in PDB)	H802 H803 F812 D840 H842 F871 L943
Binding residue (residue number reindexed from 1)	H150 H151 F160 D188 H190 F219 L291
Annotation score	1
Binding affinity	BindingDB: Kd=20nM

Enzymatic activity

Enzyme Commision number

3.5.1.98: histone deacetylase.

External links

PDB	RCSB:5a2s, PDBe:5a2s, PDBj:5a2s
PDBsum	5a2s
PubMed	26819662
UniProt	P56524\|HDAC4_HUMAN Histone deacetylase 4 (Gene Name=HDAC4)

[Back to BioLiP]