Structure of PDB 5a2s Chain A Binding Site BS01

Receptor Information

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

Receptor-Ligand Complex Structure

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Structure summary

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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)	P676 E677 R681 H802 H803 F812 D840 H842 F871 G974
Binding residue (residue number reindexed from 1)	P24 E25 R29 H150 H151 F160 D188 H190 F219 G322
Annotation score	1
Binding affinity	PDBbind-CN: -logKd/Ki=7.70,Kd=0.02uM 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)

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