Structure of PDB 5b6d Chain B Binding Site BS02

Receptor Information
>5b6d Chain B (length=317) 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
IGTYHHVVGSVHIYDSDARWAERVLDAPGFPAMPDGDNWPHVRRVLEWEE
RLRTNAARLSADALDALDLPAYWKHVVALFEAHRQVRHEDTPDRALLAAL
PEVYRQSLAVKWPGHFG
Ligand information
Ligand IDC5P
InChIInChI=1S/C9H14N3O8P/c10-5-1-2-12(9(15)11-5)8-7(14)6(13)4(20-8)3-19-21(16,17)18/h1-2,4,6-8,13-14H,3H2,(H2,10,11,15)(H2,16,17,18)/t4-,6-,7-,8-/m1/s1
InChIKeyIERHLVCPSMICTF-XVFCMESISA-N
SMILES
SoftwareSMILES
CACTVS 3.341NC1=NC(=O)N(C=C1)[CH]2O[CH](CO[P](O)(O)=O)[CH](O)[CH]2O
OpenEye OEToolkits 1.5.0C1=CN(C(=O)N=C1N)C2C(C(C(O2)COP(=O)(O)O)O)O
CACTVS 3.341NC1=NC(=O)N(C=C1)[C@@H]2O[C@H](CO[P](O)(O)=O)[C@@H](O)[C@H]2O
OpenEye OEToolkits 1.5.0C1=CN(C(=O)N=C1N)[C@H]2[C@@H]([C@@H]([C@H](O2)COP(=O)(O)O)O)O
ACDLabs 10.04O=C1N=C(N)C=CN1C2OC(C(O)C2O)COP(=O)(O)O
FormulaC9 H14 N3 O8 P
NameCYTIDINE-5'-MONOPHOSPHATE
ChEMBLCHEMBL307679
DrugBankDB03403
ZINCZINC000003861744
PDB chain5b6d 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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PDB5b6d Structural basis of the substrate preference towards CMP for a thymidylate synthase MilA involved in mildiomycin biosynthesis
Resolution1.65 Å
Binding residue
(original residue number in PDB)		R31 C155 R175 N177 D178 D186 H216 Y218
Binding residue
(residue number reindexed from 1)		R27 C151 R171 N173 D174 D182 H212 Y214
Annotation score2
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
View graph for
Cellular Component
External links
PDB RCSB:5b6d, PDBe:5b6d, PDBj:5b6d
PDBsum5b6d
PubMed28000775
UniProtB4Y380

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