Structure of PDB 2cdn Chain A Binding Site BS01

Receptor Information
>2cdn Chain A (length=186) Species: 83332 (Mycobacterium tuberculosis H37Rv) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
PRGSHMRVLLLGPPGAGKGTQAVKLAEKLGIPQISTGELFRRNIEEGTKL
GVEAKRYLDAGDLVPSDLTNELVDDRLNNPDAANGFILDGYPRSVEQAKA
LHEMLERRGTDIDAVLEFRVSEEVLLERLKGRGRADDTDDVILNRMKVYR
DETAPLLEYYRDQLKTVDAVGTMDEVFARALRALGK
Ligand information
Ligand IDADP
InChIInChI=1S/C10H15N5O10P2/c11-8-5-9(13-2-12-8)15(3-14-5)10-7(17)6(16)4(24-10)1-23-27(21,22)25-26(18,19)20/h2-4,6-7,10,16-17H,1H2,(H,21,22)(H2,11,12,13)(H2,18,19,20)/t4-,6-,7-,10-/m1/s1
InChIKeyXTWYTFMLZFPYCI-KQYNXXCUSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@](=O)(O)OP(=O)(O)O)O)O)N
CACTVS 3.341Nc1ncnc2n(cnc12)[CH]3O[CH](CO[P](O)(=O)O[P](O)(O)=O)[CH](O)[CH]3O
ACDLabs 10.04O=P(O)(O)OP(=O)(O)OCC3OC(n2cnc1c(ncnc12)N)C(O)C3O
CACTVS 3.341Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CO[P@@](O)(=O)O[P](O)(O)=O)[C@@H](O)[C@H]3O
OpenEye OEToolkits 1.5.0c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)OP(=O)(O)O)O)O)N
FormulaC10 H15 N5 O10 P2
NameADENOSINE-5'-DIPHOSPHATE
ChEMBLCHEMBL14830
DrugBankDB16833
ZINCZINC000012360703
PDB chain2cdn Chain A Residue 201 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB2cdn The Crystal Structure of Mycobacterium Tuberculosis Adenylate Kinase in Complex with Two Molecules of Adp and Mg2+ Supports an Associative Mechanism for Phosphoryl Transfer.
Resolution1.9 Å
Binding residue
(original residue number in PDB)		T31 G32 R36 L53 D57 L58 V59 T64 G85 R88 Q92 R127 R129 R140
Binding residue
(residue number reindexed from 1)		T36 G37 R41 L58 D62 L63 V64 T69 G90 R93 Q97 R132 R134 R145
Annotation score5
Enzymatic activity
Catalytic site (original residue number in PDB) K13 R88 R127 R129 R140
Catalytic site (residue number reindexed from 1) K18 R93 R132 R134 R145
Enzyme Commision number 2.7.4.3: adenylate kinase.
Gene Ontology
Molecular Function
GO:0004017 adenylate kinase activity
GO:0004550 nucleoside diphosphate kinase activity
GO:0005524 ATP binding
GO:0016301 kinase activity
GO:0019205 nucleobase-containing compound kinase activity
GO:0050145 nucleoside monophosphate kinase activity
Biological Process
GO:0006139 nucleobase-containing compound metabolic process
GO:0006144 purine nucleobase metabolic process
GO:0009123 nucleoside monophosphate metabolic process
GO:0009132 nucleoside diphosphate metabolic process
GO:0009141 nucleoside triphosphate metabolic process
GO:0009165 nucleotide biosynthetic process
GO:0016310 phosphorylation
GO:0044209 AMP salvage
GO:0046940 nucleoside monophosphate phosphorylation
Cellular Component
GO:0005737 cytoplasm
GO:0005829 cytosol
GO:0005886 plasma membrane
GO:0009274 peptidoglycan-based cell wall

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:2cdn, PDBe:2cdn, PDBj:2cdn
PDBsum2cdn
PubMed16672241
UniProtP9WKF5|KAD_MYCTU Adenylate kinase (Gene Name=adk)

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