Structure of PDB 3k8d Chain D Binding Site BS01

Receptor Information
>3k8d Chain D (length=246) Species: 562 (Escherichia coli) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
SFVVIIPARYASTRLPGKPLVDINGKPMIVHVLERARESGAERIIVATDH
EDVARAVEAAGGEVCMTRADHQSGTERLAEVVEKCAFSDDTVIVNVQGDE
PMIPATIIRQVADNLAQRQVGMATLAVPIHNAEEAFNPNAVKVVLDAEGY
ALYFSRATIPWDRDRFAEGLETVGDNFLRHLGIYGYRAGFIRRYVNWQPS
PLEHIEMLEQLRVLWYGEKIHVAVAQEVPGTGVDTPEDLERVRAEM
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 chain3k8d Chain D Residue 1243 [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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PDB3k8d Structure-based mechanism of CMP-2-keto-3-deoxymanno-octulonic acid synthetase: convergent evolution of a sugar-activating enzyme with DNA/RNA polymerases
Resolution1.9 Å
Binding residue
(original residue number in PDB)		P8 A9 R10 S13 T14 R15 K19 Q73 S74 G75 R78 Q98 G99 D100
Binding residue
(residue number reindexed from 1)		P7 A8 R9 S12 T13 R14 K18 Q72 S73 G74 R77 Q97 G98 D99
Annotation score4
Enzymatic activity
Enzyme Commision number 2.7.7.38: 3-deoxy-manno-octulosonate cytidylyltransferase.
Gene Ontology
Molecular Function
GO:0000287 magnesium ion binding
GO:0005515 protein binding
GO:0008690 3-deoxy-manno-octulosonate cytidylyltransferase activity
GO:0016779 nucleotidyltransferase activity
Biological Process
GO:0005975 carbohydrate metabolic process
GO:0009103 lipopolysaccharide biosynthetic process
GO:0019294 keto-3-deoxy-D-manno-octulosonic acid biosynthetic process
GO:0033468 CMP-keto-3-deoxy-D-manno-octulosonic acid biosynthetic process
Cellular Component
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:3k8d, PDBe:3k8d, PDBj:3k8d
PDBsum3k8d
PubMed19815542
UniProtP04951|KDSB_ECOLI 3-deoxy-manno-octulosonate cytidylyltransferase (Gene Name=kdsB)

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