Structure of PDB 5byf Chain B Binding Site BS01

Receptor Information
>5byf Chain B (length=312) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
EVAAVVVVGSCMTDLVSLTSRLPKTGETIHGHKFFIGFGGKGANQCVQAA
RLGAMTSMVCKVGKDSFGNDYIENLKQNDISTEFTYQTKDAATGTASIIV
NNEGQNIIVIVAGANLLLNTEDLRAAANVISRAKVMVCQLEITPATSLEA
LTMARRSGVKTLFNPAPAIADLDPQFYTLSDVFCCNESEAEILTGLTVGS
AADAGEAALVLLKRGCQVVIITLGAEGCVVLSQTEPEPKHIPTEKVKAVD
TTGAGDSFVGALAFYLAYYPNLSLEDMLNRSNFIAAVSVQAAGTQSSYPY
KKDLPLTLFLEH
Ligand information
Ligand IDAMP
InChIInChI=1S/C10H14N5O7P/c11-8-5-9(13-2-12-8)15(3-14-5)10-7(17)6(16)4(22-10)1-21-23(18,19)20/h2-4,6-7,10,16-17H,1H2,(H2,11,12,13)(H2,18,19,20)/t4-,6-,7-,10-/m1/s1
InChIKeyUDMBCSSLTHHNCD-KQYNXXCUSA-N
SMILES
SoftwareSMILES
CACTVS 3.370Nc1ncnc2n(cnc12)[CH]3O[CH](CO[P](O)(O)=O)[CH](O)[CH]3O
CACTVS 3.370Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CO[P](O)(O)=O)[C@@H](O)[C@H]3O
OpenEye OEToolkits 1.7.6c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)COP(=O)(O)O)O)O)N
ACDLabs 12.01O=P(O)(O)OCC3OC(n2cnc1c(ncnc12)N)C(O)C3O
OpenEye OEToolkits 1.7.6c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)O)O)O)N
FormulaC10 H14 N5 O7 P
NameADENOSINE MONOPHOSPHATE
ChEMBLCHEMBL752
DrugBankDB00131
ZINCZINC000003860156
PDB chain5byf Chain B Residue 401 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB5byf Crystal structure of human ribokinase in complex with AMP
Resolution2.0 Å
Binding residue
(original residue number in PDB)		T235 G237 A238 A267 G268 N295 A298
Binding residue
(residue number reindexed from 1)		T222 G224 A225 A254 G255 N282 A285
Annotation score4
Enzymatic activity
Catalytic site (original residue number in PDB) G266 A267 G268 D269
Catalytic site (residue number reindexed from 1) G253 A254 G255 D256
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:5byf, PDBe:5byf, PDBj:5byf
PDBsum5byf
PubMed
UniProtQ9H477|RBSK_HUMAN Ribokinase (Gene Name=RBKS)

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