Structure of PDB 3hdq Chain A Binding Site BS01

Receptor Information
>3hdq Chain A (length=365) Species: 1299 (Deinococcus radiodurans) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
QESKGFDYLIVGAGFAGSVLAERLASSGQRVLIVDRRPHIGGNAYDCYDD
AGVLIHPYGPHIFHTNSKDVFEYLSRFTEWRPYQHRVLASVDGQLLPIPI
NLDTVNRLYGLNLTSFQVEEFFASVAEKVEQVRTSEDVVVSKVGRDLYNK
FFRGYTRKQWGLDPSELDASVTARVPTRTNRDNRYFADTYQAMPLHGYTR
MFQNMLSSPNIKVMLNTDYREIADFIPFQHMIYTGPVDAFFDFCYGKLPY
RSLEFRHETHDTEQLLPTGTVNYPNDYAYTRVSEFKHITGQRHHQTSVVY
EYPRAEGDPYYPVPRPENAELYKKYEALADAAQDVTFVGRLATYRYYNMD
QVVAQALATFRRLQG
Ligand information
Ligand IDGDU
InChIInChI=1S/C15H24N2O17P2/c18-3-5-8(20)10(22)12(24)14(32-5)33-36(28,29)34-35(26,27)30-4-6-9(21)11(23)13(31-6)17-2-1-7(19)16-15(17)25/h1-2,5-6,8-14,18,20-24H,3-4H2,(H,26,27)(H,28,29)(H,16,19,25)/t5-,6-,8+,9-,10+,11-,12-,13-,14-/m1/s1
InChIKeyHSCJRCZFDFQWRP-ABVWGUQPSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0C1=CN(C(=O)NC1=O)[C@H]2[C@@H]([C@@H]([C@H](O2)CO[P@@](=O)(O)O[P@@](=O)(O)O[C@@H]3[C@@H]([C@H]([C@H]([C@H](O3)CO)O)O)O)O)O
CACTVS 3.341OC[CH]1O[CH](O[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 3.341OC[C@H]1O[C@H](O[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
ACDLabs 10.04O=P(OC1OC(C(O)C(O)C1O)CO)(O)OP(=O)(O)OCC3OC(N2C=CC(=O)NC2=O)C(O)C3O
OpenEye OEToolkits 1.5.0C1=CN(C(=O)NC1=O)C2C(C(C(O2)COP(=O)(O)OP(=O)(O)OC3C(C(C(C(O3)CO)O)O)O)O)O
FormulaC15 H24 N2 O17 P2
NameGALACTOSE-URIDINE-5'-DIPHOSPHATE;
UDP-D-GALACTOPYRANOSE
ChEMBLCHEMBL439009
DrugBankDB03501
ZINCZINC000008551104
PDB chain3hdq Chain A Residue 500 [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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PDB3hdq Structural basis of substrate binding to UDP-galactopyranose mutase: crystal structures in the reduced and oxidized state complexed with UDP-galactopyranose and UDP.
Resolution2.36 Å
Binding residue
(original residue number in PDB)		H109 F176 Y179 T180 W184 V195 R198 Y209 F210 T294 N296 R305 Y335 Y370
Binding residue
(residue number reindexed from 1)		H85 F152 Y155 T156 W160 V171 R174 Y185 F186 T270 N272 R281 Y311 Y346
Annotation score4
Binding affinityMOAD: Kd=220uM
Enzymatic activity
Catalytic site (original residue number in PDB) R198 R202 R275 R305 E325 Y370 N372
Catalytic site (residue number reindexed from 1) R174 R178 R251 R281 E301 Y346 N348
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:3hdq, PDBe:3hdq, PDBj:3hdq
PDBsum3hdq
PubMed19836401
UniProtQ9RYF1

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