Structure of PDB 3bbb Chain C Binding Site BS02

Receptor Information
>3bbb Chain C (length=148) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
ERTFIAIKPDGVQRGLVGEIIKRFEQKGFRLVAMKFLRASEEHLKQHYID
LKDRPFFPGLVKYMNSGPVVAMVWEGLNVVKTGRVMLGETNPADSKPGTI
RGDFCIQVGRNIIHGSDSVKSAEKEISLWFKPEELVDYKSCAHDWVYE
Ligand information
Ligand IDDG
InChIInChI=1S/C10H14N5O7P/c11-10-13-8-7(9(17)14-10)12-3-15(8)6-1-4(16)5(22-6)2-21-23(18,19)20/h3-6,16H,1-2H2,(H2,18,19,20)(H3,11,13,14,17)/t4-,5+,6+/m0/s1
InChIKeyLTFMZDNNPPEQNG-KVQBGUIXSA-N
SMILES
SoftwareSMILES
ACDLabs 10.04O=C1c2ncn(c2N=C(N)N1)C3OC(C(O)C3)COP(=O)(O)O
CACTVS 3.341NC1=Nc2n(cnc2C(=O)N1)[C@H]3C[C@H](O)[C@@H](CO[P](O)(O)=O)O3
CACTVS 3.341NC1=Nc2n(cnc2C(=O)N1)[CH]3C[CH](O)[CH](CO[P](O)(O)=O)O3
OpenEye OEToolkits 1.5.0c1nc2c(n1C3CC(C(O3)COP(=O)(O)O)O)N=C(NC2=O)N
OpenEye OEToolkits 1.5.0c1nc2c(n1[C@H]3C[C@@H]([C@H](O3)COP(=O)(O)O)O)N=C(NC2=O)N
FormulaC10 H14 N5 O7 P
Name2'-DEOXYGUANOSINE-5'-MONOPHOSPHATE
ChEMBLCHEMBL477487
DrugBankDB04457
ZINCZINC000001730395
PDB chain3bbb Chain C Residue 154 [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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PDB3bbb NM23-H2 may play an indirect role in transcriptional activation of c-myc gene expression but does not cleave the nuclease hypersensitive element III1.
Resolution1.3 Å
Binding residue
(original residue number in PDB)		L55 F60 L64 T94
Binding residue
(residue number reindexed from 1)		L51 F56 L60 T90
Annotation score1
Binding affinityPDBbind-CN: -logKd/Ki=7.00,Kd=100nM
Enzymatic activity
Catalytic site (original residue number in PDB) K12 Y52 N115 H118 E129
Catalytic site (residue number reindexed from 1) K8 Y48 N111 H114 E125
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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Biological Process
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Cellular Component
External links
PDB RCSB:3bbb, PDBe:3bbb, PDBj:3bbb
PDBsum3bbb
PubMed19435876
UniProtP22392|NDKB_HUMAN Nucleoside diphosphate kinase B (Gene Name=NME2)

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