Structure of PDB 5b6e Chain A Binding Site BS02

Receptor Information
>5b6e Chain A (length=319) 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
IGTYHHVVGSVHIYDSDARWAERVLDAARPGFPAMPDGDNWPHVRRVLEW
EERLRTNAARLSADALDALDLPAYWKHVVALFEAHRQVRHEDTPDRALLA
ALPEVYRQSLAVKWPGHFG
Ligand information
Ligand ID5HM
InChIInChI=1S/C10H16N3O9P/c11-8-4(2-14)1-13(10(17)12-8)9-7(16)6(15)5(22-9)3-21-23(18,19)20/h1,5-7,9,14-16H,2-3H2,(H2,11,12,17)(H2,18,19,20)/t5-,6-,7-,9-/m1/s1
InChIKeyKPUOHXMVCZBWQC-JXOAFFINSA-N
SMILES
SoftwareSMILES
CACTVS 3.385NC1=NC(=O)N(C=C1CO)[CH]2O[CH](CO[P](O)(O)=O)[CH](O)[CH]2O
ACDLabs 12.01O=P(O)(O)OCC2OC(N1C(=O)N=C(N)C(=C1)CO)C(O)C2O
OpenEye OEToolkits 1.7.6C1=C(C(=NC(=O)N1[C@H]2[C@@H]([C@@H]([C@H](O2)COP(=O)(O)O)O)O)N)CO
CACTVS 3.385NC1=NC(=O)N(C=C1CO)[C@@H]2O[C@H](CO[P](O)(O)=O)[C@@H](O)[C@H]2O
OpenEye OEToolkits 1.7.6C1=C(C(=NC(=O)N1C2C(C(C(O2)COP(=O)(O)O)O)O)N)CO
FormulaC10 H16 N3 O9 P
Name5-(hydroxymethyl)cytidine 5'-(dihydrogen phosphate);
5-hydroxymethylcytidine 5'-monophosphate
ChEMBL
DrugBank
ZINCZINC000098208520
PDB chain5b6e 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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PDB5b6e Structural basis of the substrate preference towards CMP for a thymidylate synthase MilA involved in mildiomycin biosynthesis
Resolution1.8 Å
Binding residue
(original residue number in PDB)		K133 R134
Binding residue
(residue number reindexed from 1)		K129 R130
Annotation score1
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:5b6e, PDBe:5b6e, PDBj:5b6e
PDBsum5b6e
PubMed28000775
UniProtB4Y380

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