Structure of PDB 3bbf Chain B Binding Site BS01

Receptor Information

>3bbf Chain B (length=151) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]

ANLERTFIAIKPDGVQRGLVGEIIKRFEQKGFRLVAMKFLRASEEHLKQH
YIDLKDRPFFPGLVKYMNSGPVVAMVWEGLNVVKTGRVMLGETNPADSKP
GTIRGDFCIQVGRNIIHGSDSVKSAEKEISLWFKPEELVDYKSCAHDWVY
E

Ligand information

Ligand ID

GDP

InChI

InChI=1S/C10H15N5O11P2/c11-10-13-7-4(8(18)14-10)12-2-15(7)9-6(17)5(16)3(25-9)1-24-28(22,23)26-27(19,20)21/h2-3,5-6,9,16-17H,1H2,(H,22,23)(H2,19,20,21)(H3,11,13,14,18)/t3-,5-,6-,9-/m1/s1

InChIKey

QGWNDRXFNXRZMB-UUOKFMHZSA-N

SMILES

Software	SMILES
OpenEye OEToolkits 1.7.6	c1nc2c(n1C3C(C(C(O3)COP(=O)(O)OP(=O)(O)O)O)O)N=C(NC2=O)N
CACTVS 3.385	NC1=Nc2n(cnc2C(=O)N1)[C@@H]3O[C@H](CO[P](O)(=O)O[P](O)(O)=O)[C@@H](O)[C@H]3O
CACTVS 3.385	NC1=Nc2n(cnc2C(=O)N1)[CH]3O[CH](CO[P](O)(=O)O[P](O)(O)=O)[CH](O)[CH]3O
ACDLabs 12.01	O=P(O)(O)OP(=O)(O)OCC3OC(n2cnc1c2N=C(N)NC1=O)C(O)C3O
OpenEye OEToolkits 1.7.6	c1nc2c(n1[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@](=O)(O)OP(=O)(O)O)O)O)N=C(NC2=O)N

Formula

C10 H15 N5 O11 P2

Name

GUANOSINE-5'-DIPHOSPHATE

PDB chain

3bbf Chain B Residue 160 [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	3bbf NM23-H2 may play an indirect role in transcriptional activation of c-myc gene expression but does not cleave the nuclease hypersensitive element III1.
Resolution	1.7 Å
Binding residue (original residue number in PDB)	K12 L55 F60 R88 T94 V112 G113 N115
Binding residue (residue number reindexed from 1)	K11 L54 F59 R87 T93 V111 G112 N114
Annotation score	3
Binding affinity	PDBbind-CN: -logKd/Ki=5.28,Kd=5.2uM

Enzymatic activity

Catalytic site (original residue number in PDB)	K12 Y52 N115 H118 E129
Catalytic site (residue number reindexed from 1)	K11 Y51 N114 H117 E128
Enzyme Commision number	2.7.13.3: histidine kinase. 2.7.4.6: nucleoside-diphosphate kinase.

Gene Ontology

	Molecular Function
GO:0003677	DNA binding
GO:0003713	transcription coactivator activity
GO:0004550	nucleoside diphosphate kinase activity
GO:0004673	protein histidine kinase activity
GO:0005515	protein binding
GO:0005524	ATP binding
GO:0016301	kinase activity
GO:0019003	GDP binding
GO:0042802	identical protein binding
GO:0046872	metal ion binding
GO:0051880	G-quadruplex DNA binding

	Biological Process
GO:0006183	GTP biosynthetic process
GO:0006228	UTP biosynthetic process
GO:0006241	CTP biosynthetic process
GO:0007155	cell adhesion
GO:0007229	integrin-mediated signaling pathway
GO:0009117	nucleotide metabolic process
GO:0009142	nucleoside triphosphate biosynthetic process
GO:0016310	phosphorylation
GO:0018106	peptidyl-histidine phosphorylation
GO:0042981	regulation of apoptotic process
GO:0043066	negative regulation of apoptotic process
GO:0045618	positive regulation of keratinocyte differentiation
GO:0045682	regulation of epidermis development
GO:0045893	positive regulation of DNA-templated transcription
GO:0045944	positive regulation of transcription by RNA polymerase II
GO:0050679	positive regulation of epithelial cell proliferation

	Cellular Component
GO:0001726	ruffle
GO:0005576	extracellular region
GO:0005634	nucleus
GO:0005737	cytoplasm
GO:0005829	cytosol
GO:0005925	focal adhesion
GO:0030027	lamellipodium
GO:0034774	secretory granule lumen
GO:0042995	cell projection
GO:0048471	perinuclear region of cytoplasm
GO:0070062	extracellular exosome
GO:0071944	cell periphery
GO:1904813	ficolin-1-rich granule lumen

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Molecular Function

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Cellular Component

External links

PDB	RCSB:3bbf, PDBe:3bbf, PDBj:3bbf
PDBsum	3bbf
PubMed	19435876
UniProt	P22392\|NDKB_HUMAN Nucleoside diphosphate kinase B (Gene Name=NME2)

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