Structure of PDB 3f2a Chain A Binding Site BS01

Receptor Information

>3f2a Chain A (length=277) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]

EPLESQYQVGPLLGSGGFGSVYSGIRVSDNLPVAIKHVEKDRISDWGELP
NGTRVPMEVVLLKKVSSGFSGVIRLLDWFERPDSFVLILERPEPVQDLFD
FITERGALQEELARSFFWQVLEAVRHCHNCGVLHRDIKDENILIDLNRGE
LKLIDFGSGALLKDTVYTDFDGTRVYSPPEWIRYHRYHGRSAAVWSLGIL
LYDMVCGDIPFEHDEEIIRGQVFFRQRVSSECQHLIRWCLALRPSDRPTF
EEIQNHPWMQDVLLPQETAEIHLHSLS

Ligand information

Ligand ID

985

InChI

InChI=1S/C19H22N4O2/c1-22-8-3-9-23(11-10-22)18-14-20-13-17(21-18)16-5-2-4-15(12-16)6-7-19(24)25/h2,4-7,12-14H,3,8-11H2,1H3,(H,24,25)/b7-6+

InChIKey

DTBFDAJNODVUMF-VOTSOKGWSA-N

SMILES

Software	SMILES
CACTVS 3.341	CN1CCCN(CC1)c2cncc(n2)c3cccc(\C=C\C(O)=O)c3
CACTVS 3.341	CN1CCCN(CC1)c2cncc(n2)c3cccc(C=CC(O)=O)c3
OpenEye OEToolkits 1.5.0	CN1CCCN(CC1)c2cncc(n2)c3cccc(c3)C=CC(=O)O
OpenEye OEToolkits 1.5.0	C[N@]1CCCN(CC1)c2cncc(n2)c3cccc(c3)\C=C\C(=O)O
ACDLabs 10.04	O=C(O)\C=C\c1cccc(c1)c3nc(N2CCCN(C)CC2)cnc3

Formula

C19 H22 N4 O2

Name

(2E)-3-{3-[6-(4-methyl-1,4-diazepan-1-yl)pyrazin-2-yl]phenyl}prop-2-enoic acid

PDB chain

3f2a 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	3f2a Hit to lead account of the discovery of a new class of inhibitors of Pim kinases and crystallographic studies revealing an unusual kinase binding mode.
Resolution	1.9 Å
Binding residue (original residue number in PDB)	L44 F49 A65 K67 L120 E121 L174 I185 D186
Binding residue (residue number reindexed from 1)	L13 F18 A34 K36 L89 E90 L143 I154 D155
Annotation score	1
Binding affinity	MOAD: ic50=57nM PDBbind-CN: -logKd/Ki=7.24,IC50=57nM BindingDB: IC50=57nM

Enzymatic activity

Catalytic site (original residue number in PDB)	D167 K169 N172 D186 L193 T204
Catalytic site (residue number reindexed from 1)	D136 K138 N141 D155 L162 T173
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:3f2a, PDBe:3f2a, PDBj:3f2a
PDBsum	3f2a
PubMed	19256503
UniProt	P11309\|PIM1_HUMAN Serine/threonine-protein kinase pim-1 (Gene Name=PIM1)

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