Structure of PDB 3kb2 Chain B Binding Site BS01

Receptor Information
>3kb2 Chain B (length=167) Species: 1423 (Bacillus subtilis) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
TLIILEGPDCCFKSTVAAKLSKELKYPIIKGSSFELAKSGNEKLFEHFNK
LADEDNVIIDRFVYSNLVYAKKFKDYSILTERQLRFIEDKIKAKAKVVYL
HADPSVIKKRLRVRGDEYDIDSILELYREVMSNAGLHTYSWDTGQWSSDE
IAKDIIFLVELEHHHHH
Ligand information
Ligand IDG3D
InChIInChI=1S/C10H16N5O14P3/c11-10-13-7-4(8(17)14-10)12-2-15(7)9-5(16)6(28-30(18,19)20)3(27-9)1-26-32(24,25)29-31(21,22)23/h2-3,5-6,9,16H,1H2,(H,24,25)(H2,18,19,20)(H2,21,22,23)(H3,11,13,14,17)/t3-,5-,6-,9-/m1/s1
InChIKeyHEYSFDAMRDTCJM-UUOKFMHZSA-N
SMILES
SoftwareSMILES
CACTVS 3.341NC1=Nc2n(cnc2C(=O)N1)[C@@H]3O[C@H](CO[P@@](O)(=O)O[P](O)(O)=O)[C@@H](O[P](O)(O)=O)[C@H]3O
OpenEye OEToolkits 1.5.0c1nc2c(n1[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@](=O)(O)OP(=O)(O)O)OP(=O)(O)O)O)N=C(NC2=O)N
ACDLabs 10.04O=P(O)(O)OP(=O)(O)OCC3OC(n2cnc1c2N=C(N)NC1=O)C(O)C3OP(=O)(O)O
OpenEye OEToolkits 1.5.0c1nc2c(n1C3C(C(C(O3)COP(=O)(O)OP(=O)(O)O)OP(=O)(O)O)O)N=C(NC2=O)N
CACTVS 3.341NC1=Nc2n(cnc2C(=O)N1)[CH]3O[CH](CO[P](O)(=O)O[P](O)(O)=O)[CH](O[P](O)(O)=O)[CH]3O
FormulaC10 H16 N5 O14 P3
NameGUANOSINE-3'-MONOPHOSPHATE-5'-DIPHOSPHATE
ChEMBL
DrugBankDB04121
ZINCZINC000016051736
PDB chain3kb2 Chain B Residue 180 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB3kb2 Northeast Structural Genomics Consortium Target SR256
Resolution2.2 Å
Binding residue
(original residue number in PDB)		D10 C11 C12 F13 K14 S15 T16 S152 S153
Binding residue
(residue number reindexed from 1)		D9 C10 C11 F12 K13 S14 T15 S147 S148
Annotation score2
Enzymatic activity
Enzyme Commision number ?
Gene Ontology
Molecular Function
GO:0004798 thymidylate kinase activity
Biological Process
GO:0006227 dUDP biosynthetic process
GO:0006233 dTDP biosynthetic process
GO:0006235 dTTP biosynthetic process
GO:0046940 nucleoside monophosphate phosphorylation
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:3kb2, PDBe:3kb2, PDBj:3kb2
PDBsum3kb2
PubMed
UniProtO31896|YORR_BACSU SPbeta prophage-derived uncharacterized protein YorR (Gene Name=yorR)

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