Structure of PDB 5c40 Chain A Binding Site BS01

Receptor Information
>5c40 Chain A (length=314) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
VAAVVVVGSCMTDLVSLTSRLPKTGETIHGHKFFIGFGGKGANQCVQAAR
LGAMTSMVCKVGKDSFGNDYIENLKQNDISTEFTYQTKDAATGTASIIVN
NEGQNIIVIVAGANLLLNTEDLRAAANVISRAKVMVCQLEITPATSLEAL
TMARRSGVKTLFNPAPAIADLDPQFYTLSDVFCCNESEAEILTGLTVGSA
ADAGEAALVLLKRGCQVVIITLGAEGCVVLSQTEPEPKHIPTEKVKAVDT
TGAGDSFVGALAFYLAYYPNLSLEDMLNRSNFIAAVSVQAAGTQSSYPYK
KDLPLTLFLEHHHH
Ligand information
Ligand IDACP
InChIInChI=1S/C11H18N5O12P3/c12-9-6-10(14-2-13-9)16(3-15-6)11-8(18)7(17)5(27-11)1-26-31(24,25)28-30(22,23)4-29(19,20)21/h2-3,5,7-8,11,17-18H,1,4H2,(H,22,23)(H,24,25)(H2,12,13,14)(H2,19,20,21)/t5-,7-,8-,11-/m1/s1
InChIKeyUFZTZBNSLXELAL-IOSLPCCCSA-N
SMILES
SoftwareSMILES
CACTVS 3.341Nc1ncnc2n(cnc12)[CH]3O[CH](CO[P](O)(=O)O[P](O)(=O)C[P](O)(O)=O)[CH](O)[CH]3O
ACDLabs 10.04O=P(O)(O)CP(=O)(O)OP(=O)(O)OCC3OC(n2cnc1c(ncnc12)N)C(O)C3O
OpenEye OEToolkits 1.5.0c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)OP(=O)(CP(=O)(O)O)O)O)O)N
OpenEye OEToolkits 1.5.0c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@@](=O)(O)O[P@](=O)(CP(=O)(O)O)O)O)O)N
CACTVS 3.341Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CO[P@](O)(=O)O[P@](O)(=O)C[P](O)(O)=O)[C@@H](O)[C@H]3O
FormulaC11 H18 N5 O12 P3
NamePHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER;
ADENOSINE-5'-[BETA, GAMMA-METHYLENE]TRIPHOSPHATE
ChEMBLCHEMBL133463
DrugBankDB03909
ZINCZINC000008295124
PDB chain5c40 Chain A Residue 401 [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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PDB5c40 Crystal structure of human ribokinase in complex with AMPPCP in P21 spacegroup
Resolution1.5 Å
Binding residue
(original residue number in PDB)		N199 T235 G237 A238 G240 T256 T264 A267 G268 N295 A298 A299
Binding residue
(residue number reindexed from 1)		N185 T221 G223 A224 G226 T242 T250 A253 G254 N281 A284 A285
Annotation score3
Enzymatic activity
Catalytic site (original residue number in PDB) G266 A267 G268 D269
Catalytic site (residue number reindexed from 1) G252 A253 G254 D255
Enzyme Commision number 2.7.1.15: ribokinase.
Gene Ontology
Molecular Function
GO:0004747 ribokinase activity
GO:0005515 protein binding
GO:0005524 ATP binding
GO:0016301 kinase activity
GO:0042802 identical protein binding
GO:0046872 metal ion binding
Biological Process
GO:0006014 D-ribose metabolic process
GO:0006098 pentose-phosphate shunt
GO:0006753 nucleoside phosphate metabolic process
GO:0016310 phosphorylation
GO:0019303 D-ribose catabolic process
GO:0046835 carbohydrate phosphorylation
Cellular Component
GO:0005634 nucleus
GO:0005737 cytoplasm
GO:0005829 cytosol

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:5c40, PDBe:5c40, PDBj:5c40
PDBsum5c40
PubMed
UniProtQ9H477|RBSK_HUMAN Ribokinase (Gene Name=RBKS)

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