Structure of PDB 5efh Chain D Binding Site BS02

Receptor Information

>5efh Chain D (length=356) Species: 7955 (Danio rerio) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]

ITGLVYDQRMMLHHNMWDSHHPELPQRISRIFSRHEELRLLSRCHRIPAR
LATEEELALCHSSKHISIIKSSEHMKPRDLNRLGDEYNSIFISNESYTCA
LLAAGSCFNSAQAILTGQVRNAVAIVRPPGHHAEKDTACGFCFFNTAALT
ARYAQSITRESLRVLIVDWDVHHGNGTQHIFEEDDSVLYISLHRYEDGAF
FPNSEDANYDKVGLGKGRGYNVNIPWNGGKMGDPEYMAAFHHLVMPIARE
FAPELVLVSAGFDAARGDPLGGFQVTPEGYAHLTHQLMSLAAGRVLIILE
GGYNLTSISESMSMCTSMLLGDSPPSLDHLTPLKTSATVSINNVLRAHAP
FWSSLR

Ligand information

Ligand ID

FKS

InChI

InChI=1S/C10H21F3N2O2/c11-10(12,13)9(16,17)5-2-1-3-7-15-8-4-6-14/h15-17H,1-8,14H2

InChIKey

IVRAKANOVJJYCX-UHFFFAOYSA-N

SMILES

Software	SMILES
OpenEye OEToolkits 1.9.2	C(CCC(C(F)(F)F)(O)O)CCNCCCN
CACTVS 3.385	NCCCNCCCCCC(O)(O)C(F)(F)F
ACDLabs 12.01	C(N)CCNCCCCCC(C(F)(F)F)(O)O

Formula

C10 H21 F3 N2 O2

Name

7-[(3-aminopropyl)amino]-1,1,1-trifluoroheptane-2,2-diol

PDB chain

5efh Chain D Residue 2004 [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	5efh Histone deacetylase 6 structure and molecular basis of catalysis and inhibition.
Resolution	2.162 Å
Binding residue (original residue number in PDB)	P571 H573 H574 G582 F583 D612 H614 F643 G743 Y745
Binding residue (residue number reindexed from 1)	P129 H131 H132 G140 F141 D170 H172 F201 G301 Y303
Annotation score	1
Binding affinity	MOAD: Ki=0.8uM PDBbind-CN: -logKd/Ki=6.10,Ki=800nM

Enzymatic activity

Enzyme Commision number

3.5.1.98: histone deacetylase.

External links

PDB	RCSB:5efh, PDBe:5efh, PDBj:5efh
PDBsum	5efh
PubMed	27454933
UniProt	F8W4B7

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