Structure of PDB 4z2b Chain A Binding Site BS01

Receptor Information
>4z2b Chain A (length=449) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
PPAFTELQLPRYIMAGFPVCPKLSLEFGDPASSLFRWYKEAKPGAAEPEV
GVPSSLSPSSPSSSWTETDVEERVYTPSNADIGLRLKLHCTPGDGQRFGH
SRELESVCVVEAGPGTCTFDHRHLYTKKVTEDALIRTVSYNILADTYAQT
EFSRTVLYPYCAPYALELDYRQNLIQKELTGYNADVICLQEVDRAVFSDS
LVPALEAFGLEGVFRIKQHEGLATFYRKSKFSLLSQHDISFYEALESDPL
HKELLEKLVLYPSAQEKVLQRSSVLQVSVLQSTKDSSKRICVANTHLYWH
PKGGYIRLIQMAVALAHIRHVSCDLYPGIPVIFCGDFNSTPSTGMYHFVI
NGSIPEDHEDWASNGEEERCNMSLTHFFKLKSACGEPAYTNYVGGFHGCL
DYIFIDLNALEVEQVIPLPSHEEVTTHQALPSVSHPSDHIALVCDLKWK
Ligand information
Ligand ID4LC
InChIInChI=1S/C29H25N5O3/c1-33-25-14-20(29(36)34-11-12-37-27(26(34)17-35)19-5-3-2-4-6-19)8-10-23(25)32-28(33)22-16-31-24-13-18(15-30)7-9-21(22)24/h2-10,13-14,16,26-27,31,35H,11-12,17H2,1H3/t26-,27-/m0/s1
InChIKeyBFUYKHPXWBXKQQ-SVBPBHIXSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.9.2Cn1c2cc(ccc2nc1c3c[nH]c4c3ccc(c4)C#N)C(=O)N5CCO[C@H]([C@@H]5CO)c6ccccc6
CACTVS 3.385Cn1c2cc(ccc2nc1c3c[nH]c4cc(ccc34)C#N)C(=O)N5CCO[CH]([CH]5CO)c6ccccc6
ACDLabs 12.01c2(ccc1nc(n(C)c1c2)c3cnc4c3ccc(c4)C#N)C(N6CCOC(c5ccccc5)C6CO)=O
OpenEye OEToolkits 1.9.2Cn1c2cc(ccc2nc1c3c[nH]c4c3ccc(c4)C#N)C(=O)N5CCOC(C5CO)c6ccccc6
CACTVS 3.385Cn1c2cc(ccc2nc1c3c[nH]c4cc(ccc34)C#N)C(=O)N5CCO[C@H]([C@@H]5CO)c6ccccc6
FormulaC29 H25 N5 O3
Name3-(6-{[(2S,3S)-3-(hydroxymethyl)-2-phenylmorpholin-4-yl]carbonyl}-1-methyl-1H-benzimidazol-2-yl)-1H-indole-6-carbonitrile
ChEMBL
DrugBank
ZINCZINC000230585846
PDB chain4z2b Chain A Residue 705 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

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PDB4z2b The Role of Phosphodiesterase 12 (PDE12) as a Negative Regulator of the Innate Immune Response and the Discovery of Antiviral Inhibitors.
Resolution1.8 Å
Binding residue
(original residue number in PDB)		Y307 E351 W459 P461 N498 F556
Binding residue
(residue number reindexed from 1)		Y147 E191 W299 P301 N338 F396
Annotation score1
Binding affinityMOAD: Ki=17.5nM
PDBbind-CN: -logKd/Ki=7.76,Ki=17.5nM
Enzymatic activity
Enzyme Commision number 3.1.13.4: poly(A)-specific ribonuclease.
3.1.4.-
Gene Ontology
Molecular Function
GO:0003824 catalytic activity

View graph for
Molecular Function
External links
PDB RCSB:4z2b, PDBe:4z2b, PDBj:4z2b
PDBsum4z2b
PubMed26055709
UniProtQ6L8Q7|PDE12_HUMAN 2',5'-phosphodiesterase 12 (Gene Name=PDE12)

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