Structure of PDB 3mj4 Chain D Binding Site BS01

Receptor Information
>3mj4 Chain D (length=359) Species: 243230 (Deinococcus radiodurans R1 = ATCC 13939 = DSM 20539) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
FDYLIVGAGFAGSVLAERLASSGQRVLIVDRRPHIGGNAYDCYDDAGVLI
HPYGPHIFHTNSKDVFEYLSRFTEWRPYQHRVLASVDGQLLPIPINLDTV
NRLYGLNLTSFQVEEFFASVAEKVEQVRTSEDVVVSKVGRDLYNKFFRGY
TRKQWGLDPSELDASVTARVPTRTNRDNRYFADTYQAMPLHGYTRMFQNM
LSSPNIKVMLNTDYREIADFIPFQHMIYTGPVDAFFDFCYGKLPYRSLEF
RHETHDTEQLLPTGTVNYPNDYAYTRVSEFKHITGQRHHQTSVVYEYPRA
EGDPYYPVPRPENAELYKKYEALADAAQDVTFVGRLATYRYYNMDQVVAQ
ALATFRRLQ
Ligand information
Ligand IDURM
InChIInChI=1S/C16H26N2O16P2/c19-3-6-10(21)13(24)12(23)8(32-6)5-35(27,28)34-36(29,30)31-4-7-11(22)14(25)15(33-7)18-2-1-9(20)17-16(18)26/h1-2,6-8,10-15,19,21-25H,3-5H2,(H,27,28)(H,29,30)(H,17,20,26)/t6-,7-,8-,10+,11-,12+,13+,14-,15-/m1/s1
InChIKeyWUPLBUVQIJIOHV-PPSAJGQHSA-N
SMILES
SoftwareSMILES
CACTVS 3.370OC[CH]1O[CH](C[P](O)(=O)O[P](O)(=O)OC[CH]2O[CH]([CH](O)[CH]2O)N3C=CC(=O)NC3=O)[CH](O)[CH](O)[CH]1O
CACTVS 3.370OC[C@H]1O[C@H](C[P](O)(=O)O[P](O)(=O)OC[C@H]2O[C@H]([C@H](O)[C@@H]2O)N3C=CC(=O)NC3=O)[C@H](O)[C@@H](O)[C@H]1O
OpenEye OEToolkits 1.7.0C1=CN(C(=O)NC1=O)C2C(C(C(O2)COP(=O)(O)OP(=O)(CC3C(C(C(C(O3)CO)O)O)O)O)O)O
OpenEye OEToolkits 1.7.0C1=CN(C(=O)NC1=O)[C@H]2[C@@H]([C@@H]([C@H](O2)CO[P@@](=O)(O)O[P@@](=O)(C[C@@H]3[C@@H]([C@H]([C@H]([C@H](O3)CO)O)O)O)O)O)O
FormulaC16 H26 N2 O16 P2
Name(((2S,3R,4S,5R,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)tetrahydro-2H-pyran-2-yl)methyl)phosphonic (((2R,3S,4R,5R)-5-(2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)-3,4-dihydroxytetrahydrofuran-2-yl)methyl phosphoric) anhydride;
Uridine diphospho methylene galactopyranose
ChEMBL
DrugBank
ZINCZINC000064436301
PDB chain3mj4 Chain D Residue 600 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB3mj4 Chemoenzymatic Synthesis, Inhibition Studies, and X-ray Crystallographic Analysis of the Phosphono Analog of UDP-Galp as an Inhibitor and Mechanistic Probe for UDP-Galactopyranose Mutase.
Resolution2.65 Å
Binding residue
(original residue number in PDB)
I122 F175 F176 Y179 T180 W184 V195 V199 Y209 F210 R305
Binding residue
(residue number reindexed from 1)
I93 F146 F147 Y150 T151 W155 V166 V170 Y180 F181 R276
Annotation score3
Enzymatic activity
Catalytic site (original residue number in PDB) R198 R202 R275 R305 E325 Y370 N372
Catalytic site (residue number reindexed from 1) R169 R173 R246 R276 E296 Y341 N343
Enzyme Commision number 5.4.99.9: UDP-galactopyranose mutase.
Gene Ontology
Molecular Function
GO:0000166 nucleotide binding
GO:0008767 UDP-galactopyranose mutase activity
GO:0016853 isomerase activity
GO:0050660 flavin adenine dinucleotide binding
Cellular Component
GO:0005829 cytosol

View graph for
Molecular Function

View graph for
Cellular Component
External links
PDB RCSB:3mj4, PDBe:3mj4, PDBj:3mj4
PDBsum3mj4
PubMed20850454
UniProtQ9RYF1

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