Structure of PDB 5jp9 Chain B Binding Site BS02

Receptor Information
>5jp9 Chain B (length=318) Species: 504097 (Streptomyces rimofaciens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
TFGTFQDAYLSQLRDIYHSPEFRNAPRGQASRERIGAGFRLLDPVQRHIS
VPARRANVVFNFAEALWYLSGSDRLDFIQYYAPGIAAYSADGRTLRGTAY
GPRIFRHPAGGVNQWENVVKTLTDDPDSKRAVIQIFDPRELAVADNIDVA
CTLALQFLIRDGLLCGIGYMRANDAFRGAVSDVFSFTFLQEFTARYLGLG
IGTYHHVVGSVHIYDSDARWAERVLDARPGFPAMPDGDNWPHVRRVLEWE
ERLRTNAARLSADALDALDLPAYWKHVVALFEAHRQVRHEDTPDRALLAA
LPEVYRQSLAVKWPGHFG
Ligand information
Ligand IDDCM
InChIInChI=1S/C9H14N3O7P/c10-7-1-2-12(9(14)11-7)8-3-5(13)6(19-8)4-18-20(15,16)17/h1-2,5-6,8,13H,3-4H2,(H2,10,11,14)(H2,15,16,17)/t5-,6+,8+/m0/s1
InChIKeyNCMVOABPESMRCP-SHYZEUOFSA-N
SMILES
SoftwareSMILES
CACTVS 3.341NC1=NC(=O)N(C=C1)[C@H]2C[C@H](O)[C@@H](CO[P](O)(O)=O)O2
CACTVS 3.341NC1=NC(=O)N(C=C1)[CH]2C[CH](O)[CH](CO[P](O)(O)=O)O2
OpenEye OEToolkits 1.5.0C1C(C(OC1N2C=CC(=NC2=O)N)COP(=O)(O)O)O
ACDLabs 10.04O=C1N=C(N)C=CN1C2OC(C(O)C2)COP(=O)(O)O
OpenEye OEToolkits 1.5.0C1[C@@H]([C@H](O[C@H]1N2C=CC(=NC2=O)N)COP(=O)(O)O)O
FormulaC9 H14 N3 O7 P
Name2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE
ChEMBLCHEMBL374699
DrugBankDB03798
ZINCZINC000003861759
PDB chain5jp9 Chain B Residue 401 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB5jp9 Structural basis of the substrate preference towards CMP for a thymidylate synthase MilA involved in mildiomycin biosynthesis
Resolution2.101 Å
Binding residue
(original residue number in PDB)		R31 Y104 C155 R175 N177 D178 D186 H216
Binding residue
(residue number reindexed from 1)		R27 Y100 C151 R171 N173 D174 D182 H212
Annotation score3
Enzymatic activity
Catalytic site (original residue number in PDB) E68
Catalytic site (residue number reindexed from 1) E64
Enzyme Commision number ?
Gene Ontology
Molecular Function
GO:0004799 thymidylate synthase activity
GO:0008168 methyltransferase activity
GO:0016741 transferase activity, transferring one-carbon groups
Biological Process
GO:0006231 dTMP biosynthetic process
GO:0032259 methylation
Cellular Component
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:5jp9, PDBe:5jp9, PDBj:5jp9
PDBsum5jp9
PubMed28000775
UniProtB4Y380

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