Structure of PDB 5c3y Chain K Binding Site BS01

Receptor Information
>5c3y Chain K (length=312) 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
KDLPLTLFLEHH
Ligand information
Ligand IDAN2
InChIInChI=1S/C10H16N6O9P2/c11-8-5-9(14-2-13-8)16(3-15-5)10-7(18)6(17)4(24-10)1-23-27(21,22)25-26(12,19)20/h2-4,6-7,10,17-18H,1H2,(H,21,22)(H2,11,13,14)(H3,12,19,20)/t4-,6-,7-,10-/m1/s1
InChIKeyFQMDCEJHLOLKLI-KQYNXXCUSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)OP(=O)(N)O)O)O)N
ACDLabs 10.04O=P(O)(OP(=O)(O)OCC3OC(n2cnc1c(ncnc12)N)C(O)C3O)N
CACTVS 3.341Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CO[P@@](O)(=O)O[P@](N)(O)=O)[C@@H](O)[C@H]3O
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)(N)O)O)O)N
CACTVS 3.341Nc1ncnc2n(cnc12)[CH]3O[CH](CO[P](O)(=O)O[P](N)(O)=O)[CH](O)[CH]3O
FormulaC10 H16 N6 O9 P2
NameAMP PHOSPHORAMIDATE
ChEMBLCHEMBL574810
DrugBank
ZINC
PDB chain5c3y Chain K 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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PDB5c3y Structure of human ribokinase crystallized with AMPPNP
Resolution2.6 Å
Binding residue
(original residue number in PDB)		T235 G237 A238 G240 V259 T264 A267 G268 N295 A298 A299
Binding residue
(residue number reindexed from 1)		T221 G223 A224 G226 V245 T250 A253 G254 N281 A284 A285
Annotation score4
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:5c3y, PDBe:5c3y, PDBj:5c3y
PDBsum5c3y
PubMed
UniProtQ9H477|RBSK_HUMAN Ribokinase (Gene Name=RBKS)

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