Structure of PDB 1bpj Chain A Binding Site BS01
Receptor Information
>1bpj Chain A (length=316) Species:
1582
(Lacticaseibacillus casei) [
Search protein sequence
] [
Download receptor structure
] [
Download structure with residue number starting from 1
] [
View receptor structure
]
MLEQPYLDLAKKVLDEGHFKPDRTHTGTYSIFGHQMRFDLSKGFPLLTTK
KVPFGLIKSELLWFLHGDTNIRFLLQHRNHIWDEWAFEKWVKSDEYHGPD
MTDFGHRSQKDPEFAAVYHEEMAKFDDRVLHDDAFAAKYGDLGLVYGSQW
RAWHTSKGDTIDQLGDVIEQIKTHPYSTTLIVSAWNPEDVPTMALPPCHT
LYQFYVNDGKLSLQLYQRSADIFLGVPFNIASYALLTHLVAHECGLEVGE
FIHTFGDAHLYVNHLDQIKEQLSRTPRPAPTLQLNPDKHDIFDFDMKDIK
LLNYDPYPAIKAPVAV
Ligand information
Ligand ID
UMP
InChI
InChI=1S/C9H13N2O8P/c12-5-3-8(11-2-1-7(13)10-9(11)14)19-6(5)4-18-20(15,16)17/h1-2,5-6,8,12H,3-4H2,(H,10,13,14)(H2,15,16,17)/t5-,6+,8+/m0/s1
InChIKey
JSRLJPSBLDHEIO-SHYZEUOFSA-N
SMILES
Software
SMILES
ACDLabs 12.01
O=P(O)(O)OCC2OC(N1C(=O)NC(=O)C=C1)CC2O
CACTVS 3.370
O[CH]1C[CH](O[CH]1CO[P](O)(O)=O)N2C=CC(=O)NC2=O
OpenEye OEToolkits 1.7.6
C1[C@@H]([C@H](O[C@H]1N2C=CC(=O)NC2=O)COP(=O)(O)O)O
CACTVS 3.370
O[C@H]1C[C@@H](O[C@@H]1CO[P](O)(O)=O)N2C=CC(=O)NC2=O
OpenEye OEToolkits 1.7.6
C1C(C(OC1N2C=CC(=O)NC2=O)COP(=O)(O)O)O
Formula
C9 H13 N2 O8 P
Name
2'-DEOXYURIDINE 5'-MONOPHOSPHATE;
DUMP
ChEMBL
CHEMBL211312
DrugBank
DB03800
ZINC
ZINC000004228260
PDB chain
1bpj Chain A Residue 318 [
Download ligand structure
] [
Download structure with residue number starting from 1
] [
View ligand structure
]
Receptor-Ligand Complex Structure
Global view
Local view
Structure summary
[
Spin on
] [
Spin off
] [
Reset
]
[
High quality
] [
Low quality
]
[
White background
] [
Black background
]
[
Spin on
] [
Spin off
] [
Reset
]
[
High quality
] [
Low quality
]
[
White background
] [
Black background
]
PDB
1bpj
Energetic contributions of four arginines to phosphate-binding in thymidylate synthase are more than additive and depend on optimization of "effective charge balance".
Resolution
2.4 Å
Binding residue
(original residue number in PDB)
R23 S219 A220 D221 N229 H259 Y261
Binding residue
(residue number reindexed from 1)
R23 S219 A220 D221 N229 H259 Y261
Annotation score
3
Enzymatic activity
Catalytic site (original residue number in PDB)
E60 W82 Y146 C198 R218 D221
Catalytic site (residue number reindexed from 1)
E60 W82 Y146 C198 R218 D221
Enzyme Commision number
2.1.1.45
: thymidylate synthase.
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:0006235
dTTP biosynthetic process
GO:0009165
nucleotide biosynthetic process
GO:0032259
methylation
Cellular Component
GO:0005737
cytoplasm
GO:0005829
cytosol
View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB
RCSB:1bpj
,
PDBe:1bpj
,
PDBj:1bpj
PDBsum
1bpj
PubMed
10653645
UniProt
P00469
|TYSY_LACCA Thymidylate synthase (Gene Name=thyA)
[
Back to BioLiP
]