Structure of PDB 1b5d Chain B Binding Site BS01

Receptor Information
>1b5d Chain B (length=246) Species: 10665 (Tequatrovirus T4) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MISDSMTVEEIRLHLGLALKEKDFVVDKTGVKTIEIIGASFVADEPFIFG
ALNDEYIQRELEWYKSKSLFVKDIPGETPKIWQQVASSKGEINSNYGWAI
WSEDNYAQYDMCLAELGQNPDSRRGIMIYTRPSMQFDYNKDGMSDFMCTN
TVQYLIRDKKINAVVNMRSNDVVFGFRNDYAWQKYVLDKLVSDLNAGDST
RQYKAGSIIWNVGSLHVYSRHFYLVDHWWKTGETHISKKDYVGKYA
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 chain1b5d Chain A Residue 300 [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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PDB1b5d Crystal structure of deoxycytidylate hydroxymethylase from bacteriophage T4, a component of the deoxyribonucleoside triphosphate-synthesizing complex.
Resolution2.2 Å
Binding residue
(original residue number in PDB)		R123 R124
Binding residue
(residue number reindexed from 1)		R123 R124
Annotation score4
Enzymatic activity
Catalytic site (original residue number in PDB) E60 C148 D179
Catalytic site (residue number reindexed from 1) E60 C148 D179
Enzyme Commision number 2.1.2.8: deoxycytidylate 5-hydroxymethyltransferase.
Gene Ontology
Molecular Function
GO:0016740 transferase activity
GO:0047153 deoxycytidylate 5-hydroxymethyltransferase activity

View graph for
Molecular Function
External links
PDB RCSB:1b5d, PDBe:1b5d, PDBj:1b5d
PDBsum1b5d
PubMed10064578
UniProtP08773|DCHM_BPT4 Deoxycytidylate 5-hydroxymethyltransferase (Gene Name=42)

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