Structure of PDB 3vbq Chain A Binding Site BS01

Receptor Information

>3vbq Chain A (length=271) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]

ESQYQVGPLLGSGGFGSVYSGIRVSDNLPVAIKHVEKDRISDWGELPNGT
RVPMEVVLLKKVSSGFSGVIRLLDWFERPDSFVLILERPEPVQDLFDFIT
ERGALQEELARSFFWQVLEAVRHCHNCGVLHRDIKDENILIDLNRGELKL
IDFGSGALLKDTVYTDFDGTRVYSPPEWIRYHRYHGRSAAVWSLGILLYD
MVCGDIPFEHDEEIIRGQVFFRQRVSSECQHLIRWCLALRPSDRPTFEEI
QNHPWMQDVLLPQETAEIHLH

Ligand information

Ligand ID

0F5

InChI

InChI=1S/C20H21N5O2S/c21-14-4-6-15(7-5-14)23-18-11-22-10-16(24-18)13-3-1-2-12(8-13)9-17-19(26)25-20(27)28-17/h1-3,8-11,14-15H,4-7,21H2,(H,23,24)(H,25,26,27)/b17-9-/t14-,15-

InChIKey

UKPXIONZHWFMAU-MDYDWWASSA-N

SMILES

Software	SMILES
OpenEye OEToolkits 2.0.7	c1cc(cc(c1)c2cncc(n2)NC3CCC(CC3)N)/C=C\4/C(=O)NC(=O)S4
CACTVS 3.385	N[C@H]1CC[C@@H](CC1)Nc2cncc(n2)c3cccc(/C=C/4SC(=O)NC/4=O)c3
OpenEye OEToolkits 2.0.7	c1cc(cc(c1)c2cncc(n2)NC3CCC(CC3)N)C=C4C(=O)NC(=O)S4
CACTVS 3.385	N[CH]1CC[CH](CC1)Nc2cncc(n2)c3cccc(C=C4SC(=O)NC4=O)c3

Formula

C20 H21 N5 O2 S

Name

(5~{Z})-5-[[3-[6-[(4-azanylcyclohexyl)amino]pyrazin-2-yl]phenyl]methylidene]-1,3-thiazolidine-2,4-dione

PDB chain

3vbq Chain A Residue 555 [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	3vbq Implications of promiscuous Pim-1 kinase fragment inhibitor hydrophobic interactions for fragment-based drug design.
Resolution	1.85 Å
Binding residue (original residue number in PDB)	F49 V52 A65 K67 L120 E121 L174 I185 D186
Binding residue (residue number reindexed from 1)	F15 V18 A31 K33 L86 E87 L140 I151 D152
Annotation score	1
Binding affinity	MOAD: ic50=470pM PDBbind-CN: -logKd/Ki=9.33,IC50=470pM

Enzymatic activity

Catalytic site (original residue number in PDB)	D167 K169 N172 D186 L193 T204
Catalytic site (residue number reindexed from 1)	D133 K135 N138 D152 L159 T170
Enzyme Commision number	2.7.11.1: non-specific serine/threonine protein kinase.

Gene Ontology

	Molecular Function
GO:0004672	protein kinase activity
GO:0004674	protein serine/threonine kinase activity
GO:0005515	protein binding
GO:0005524	ATP binding
GO:0008134	transcription factor binding
GO:0030145	manganese ion binding
GO:0043024	ribosomal small subunit binding
GO:0044024	histone H2AS1 kinase activity
GO:0046872	metal ion binding
GO:0106310	protein serine kinase activity

	Biological Process
GO:0006338	chromatin remodeling
GO:0006468	protein phosphorylation
GO:0006915	apoptotic process
GO:0016310	phosphorylation
GO:0022898	regulation of transmembrane transporter activity
GO:0043066	negative regulation of apoptotic process
GO:0043433	negative regulation of DNA-binding transcription factor activity
GO:0045824	negative regulation of innate immune response
GO:0045893	positive regulation of DNA-templated transcription
GO:0046777	protein autophosphorylation
GO:0050821	protein stabilization
GO:0060045	positive regulation of cardiac muscle cell proliferation
GO:0070561	vitamin D receptor signaling pathway
GO:0071346	cellular response to type II interferon
GO:0090336	positive regulation of brown fat cell differentiation
GO:1902033	regulation of hematopoietic stem cell proliferation
GO:1904263	positive regulation of TORC1 signaling
GO:1905062	positive regulation of cardioblast proliferation
GO:1990748	cellular detoxification

	Cellular Component
GO:0005634	nucleus
GO:0005654	nucleoplasm
GO:0005730	nucleolus
GO:0005737	cytoplasm
GO:0005829	cytosol
GO:0005886	plasma membrane

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Molecular Function

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Biological Process

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Cellular Component

External links

PDB	RCSB:3vbq, PDBe:3vbq, PDBj:3vbq
PDBsum	3vbq
PubMed	22339127
UniProt	P11309\|PIM1_HUMAN Serine/threonine-protein kinase pim-1 (Gene Name=PIM1)

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