Structure of PDB 3mj4 Chain D Binding Site BS02

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 IDFAD
InChIInChI=1S/C27H33N9O15P2/c1-10-3-12-13(4-11(10)2)35(24-18(32-12)25(42)34-27(43)33-24)5-14(37)19(39)15(38)6-48-52(44,45)51-53(46,47)49-7-16-20(40)21(41)26(50-16)36-9-31-17-22(28)29-8-30-23(17)36/h3-4,8-9,14-16,19-21,26,37-41H,5-7H2,1-2H3,(H,44,45)(H,46,47)(H2,28,29,30)(H,34,42,43)/t14-,15+,16+,19-,20+,21+,26+/m0/s1
InChIKeyVWWQXMAJTJZDQX-UYBVJOGSSA-N
SMILES
SoftwareSMILES
CACTVS 3.341Cc1cc2N=C3C(=O)NC(=O)N=C3N(C[C@H](O)[C@H](O)[C@H](O)CO[P@](O)(=O)O[P@@](O)(=O)OC[C@H]4O[C@H]([C@H](O)[C@@H]4O)n5cnc6c(N)ncnc56)c2cc1C
OpenEye OEToolkits 1.5.0Cc1cc2c(cc1C)N(C3=NC(=O)NC(=O)C3=N2)CC(C(C(COP(=O)(O)OP(=O)(O)OCC4C(C(C(O4)n5cnc6c5ncnc6N)O)O)O)O)O
OpenEye OEToolkits 1.5.0Cc1cc2c(cc1C)N(C3=NC(=O)NC(=O)C3=N2)C[C@@H]([C@@H]([C@@H](CO[P@@](=O)(O)O[P@](=O)(O)OC[C@@H]4[C@H]([C@H]([C@@H](O4)n5cnc6c5ncnc6N)O)O)O)O)O
CACTVS 3.341Cc1cc2N=C3C(=O)NC(=O)N=C3N(C[CH](O)[CH](O)[CH](O)CO[P](O)(=O)O[P](O)(=O)OC[CH]4O[CH]([CH](O)[CH]4O)n5cnc6c(N)ncnc56)c2cc1C
ACDLabs 10.04O=C2C3=Nc1cc(c(cc1N(C3=NC(=O)N2)CC(O)C(O)C(O)COP(=O)(O)OP(=O)(O)OCC6OC(n5cnc4c(ncnc45)N)C(O)C6O)C)C
FormulaC27 H33 N9 O15 P2
NameFLAVIN-ADENINE DINUCLEOTIDE
ChEMBLCHEMBL1232653
DrugBankDB03147
ZINCZINC000008215434
PDB chain3mj4 Chain D Residue 450 [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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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)		V35 G36 G38 A40 D59 R60 R61 N67 H85 I86 D242 Y243 Y334 G363 R364 Y370 Y371 N372 M373 V376
Binding residue
(residue number reindexed from 1)		V6 G7 G9 A11 D30 R31 R32 N38 H56 I57 D213 Y214 Y305 G334 R335 Y341 Y342 N343 M344 V347
Annotation score1
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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