Structure of PDB 8fvd Chain A Binding Site BS01

Receptor Information
>8fvd Chain A (length=533) Species: 562 (Escherichia coli) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MTTNYIFVTGGVVSSLGKGIAAASLAAILEARGLNVTIMKLDPYINVDPG
TMSPIQHGEVFVTEDGAETDLDLGHYERFIRTKMSRRNNFTTGRIYSDVL
RKERRGDYLGATVQVIPHITNAIKERVLEGGEGHDVVLVEIGGTVGDIES
LPFLEAIRQMAVEIGREHTLFMHLTLVPYMAASGEVKTKPTQHSVKELLS
IGIQPDILICRSDRAVPANERAKIALFCNVPEKAVISLKDVDSIYKIPGL
LKSQGLDDYICKRFSLNCPEANLSEWEQVIFEEANPVSEVTIGMVGKYIE
LPDAYKSVIEALKHGGLKNRVSVNIKLIDSQDVETRGVEILKGLDAILVP
GGFGYRGVEGMITTARFARENNIPYLGICLGMQVALIDYARHVANMENAN
STEFVPDCKYPVVALITEWRDENGNVEVMRLGAQQCQLVDDSLVRQLYNA
PTIVERHRHRYEVNNMLLKQIEDAGLRVAGRSGDDQLVEIIEVPNHPWFV
ACQFHPEFTSTPRDGHPLFAGFVKAASEFQKRQ
Ligand information
Ligand IDGTF
InChIInChI=1S/C9H14F2N3O13P3/c10-9(11)6(15)4(25-7(9)14-2-1-5(12)13-8(14)16)3-24-29(20,21)27-30(22,23)26-28(17,18)19/h1-2,4,6-7,15H,3H2,(H,20,21)(H,22,23)(H2,12,13,16)(H2,17,18,19)/t4-,6-,7-/m1/s1
InChIKeyYMOXEIOKAJSRQX-QPPQHZFASA-N
SMILES
SoftwareSMILES
CACTVS 3.385NC1=NC(=O)N(C=C1)[C@@H]2O[C@H](CO[P](O)(=O)O[P](O)(=O)O[P](O)(O)=O)[C@@H](O)C2(F)F
ACDLabs 12.01FC2(F)C(N1C(=O)N=C(N)C=C1)OC(C2O)COP(OP(O)(=O)OP(O)(O)=O)(O)=O
OpenEye OEToolkits 2.0.6C1=CN(C(=O)N=C1N)[C@H]2C([C@@H]([C@H](O2)COP(=O)(O)OP(=O)(O)OP(=O)(O)O)O)(F)F
OpenEye OEToolkits 2.0.6C1=CN(C(=O)N=C1N)C2C(C(C(O2)COP(=O)(O)OP(=O)(O)OP(=O)(O)O)O)(F)F
CACTVS 3.385NC1=NC(=O)N(C=C1)[CH]2O[CH](CO[P](O)(=O)O[P](O)(=O)O[P](O)(O)=O)[CH](O)C2(F)F
FormulaC9 H14 F2 N3 O13 P3
Name2'-deoxy-2',2'-difluorocytidine 5'-(tetrahydrogen triphosphate);
Gemcitabine-TRIPHOSPHATE
ChEMBLCHEMBL1201383
DrugBank
ZINCZINC000013546270
PDB chain8fvd Chain A Residue 602 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB8fvd A metal-dependent conformational change provides a structural basis for the inhibition of CTP synthase by gemcitabine-5'-triphosphate.
Resolution2.38 Å
Binding residue
(original residue number in PDB)		K187 T188 K189 Q192 K223
Binding residue
(residue number reindexed from 1)		K187 T188 K189 Q192 K223
Annotation score2
Enzymatic activity
Enzyme Commision number 6.3.4.2: CTP synthase (glutamine hydrolyzing).
Gene Ontology
Molecular Function
GO:0000287 magnesium ion binding
GO:0003883 CTP synthase activity
GO:0004359 glutaminase activity
GO:0005524 ATP binding
GO:0016874 ligase activity
GO:0042802 identical protein binding
GO:0046872 metal ion binding
Biological Process
GO:0006221 pyrimidine nucleotide biosynthetic process
GO:0006241 CTP biosynthetic process
GO:0006541 glutamine metabolic process
GO:0019856 pyrimidine nucleobase biosynthetic process
GO:0044210 'de novo' CTP biosynthetic process
GO:0051289 protein homotetramerization
Cellular Component
GO:0005737 cytoplasm
GO:0005829 cytosol
GO:0032991 protein-containing complex
GO:0097268 cytoophidium

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Molecular Function
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Biological Process
View graph for
Cellular Component
External links
PDB RCSB:8fvd, PDBe:8fvd, PDBj:8fvd
PDBsum8fvd
PubMed37106216
UniProtP0A7E5|PYRG_ECOLI CTP synthase (Gene Name=pyrG)

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