Structure of PDB 6pk7 Chain D Binding Site BS03

Receptor Information
>6pk7 Chain D (length=557) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MKYILVTGGVISGIGKGIIASSIGTILKSCGLRVTAIKIDPYINIDAGTF
SPYEHGEVFVLNDGGEVDLDLGNYERFLDINLYKDNNITTGKIYQHVINK
ERRGDYLGKTVQVVPHITDAVQEWVMNQAKVPVDGNKEEPQICVIELGGT
IGDIEGMPFVEAFRQFQFKAKRENFCNIHVSLVPQLSATGEQKTKPTQNS
VRALRGLGLSPDLIVCRSSTPIEMAVKEKISMFCHVNPEQVICIHDVSST
YRVPVLLEEQSIVKYFKERLHLPIGDSASNLLFKWRNMADRYERLQKICS
IALVGKYTKLRDCYASVFKALEHSALAINHKLNLMYIDSIDLEKITETED
PVKFHEAWQKLCKADGILVPGGFGIRGTLGKLQAISWARTKKIPFLGVCL
GMQLAVIEFARNCLNLKDADSTEFRPNAPVPLVIDMPEHNPGNLGGTMRL
GIRRTVFKTENSILRKLYGDVPFIEERHRHRFEVNPNLIKQFEQNDLSFV
GQDVDGDRMEIIELANHPYFVGVQFHPEFSSRPMKPSPPYLGLLLAATGN
LNAYLQQ
Ligand information
Ligand IDCTP
InChIInChI=1S/C9H16N3O14P3/c10-5-1-2-12(9(15)11-5)8-7(14)6(13)4(24-8)3-23-28(19,20)26-29(21,22)25-27(16,17)18/h1-2,4,6-8,13-14H,3H2,(H,19,20)(H,21,22)(H2,10,11,15)(H2,16,17,18)/t4-,6-,7-,8-/m1/s1
InChIKeyPCDQPRRSZKQHHS-XVFCMESISA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0C1=CN(C(=O)N=C1N)C2C(C(C(O2)COP(=O)(O)OP(=O)(O)OP(=O)(O)O)O)O
OpenEye OEToolkits 1.5.0C1=CN(C(=O)N=C1N)[C@H]2[C@@H]([C@@H]([C@H](O2)CO[P@](=O)(O)O[P@](=O)(O)OP(=O)(O)O)O)O
CACTVS 3.341NC1=NC(=O)N(C=C1)[CH]2O[CH](CO[P](O)(=O)O[P](O)(=O)O[P](O)(O)=O)[CH](O)[CH]2O
ACDLabs 10.04O=P(O)(O)OP(=O)(O)OP(=O)(O)OCC2OC(N1C(=O)N=C(N)C=C1)C(O)C2O
CACTVS 3.341NC1=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)[C@H]2O
FormulaC9 H16 N3 O14 P3
NameCYTIDINE-5'-TRIPHOSPHATE
ChEMBLCHEMBL223533
DrugBankDB02431
ZINCZINC000003861746
PDB chain6pk7 Chain D Residue 602 [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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PDB6pk7 Coupled structural transitions enable highly cooperative regulation of human CTPS2 filaments.
Resolution3.1 Å
Binding residue
(original residue number in PDB)		D153 I154 E155
Binding residue
(residue number reindexed from 1)		D153 I154 E155
Annotation score4
Binding affinityPDBbind-CN: -logKd/Ki=4.72,IC50=19.2uM
Enzymatic activity
Enzyme Commision number 6.3.4.2: CTP synthase (glutamine hydrolyzing).
Gene Ontology
Molecular Function
GO:0003883 CTP synthase activity
GO:0005515 protein binding
GO:0005524 ATP binding
GO:0016874 ligase activity
GO:0042802 identical protein binding
Biological Process
GO:0006220 pyrimidine nucleotide metabolic process
GO:0006221 pyrimidine nucleotide biosynthetic process
GO:0006241 CTP biosynthetic process
GO:0006541 glutamine metabolic process
GO:0019637 organophosphate metabolic process
GO:0019856 pyrimidine nucleobase biosynthetic process
GO:0044210 'de novo' CTP biosynthetic process
Cellular Component
GO:0005737 cytoplasm
GO:0005739 mitochondrion
GO:0005829 cytosol
GO:0097268 cytoophidium

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:6pk7, PDBe:6pk7, PDBj:6pk7
PDBsum6pk7
PubMed31873303
UniProtQ9NRF8|PYRG2_HUMAN CTP synthase 2 (Gene Name=CTPS2)

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