Structure of PDB 4bkp Chain B Binding Site BS01

Receptor Information
>4bkp Chain B (length=324) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
DLGTENLYFQSMRILVTGGSGLVGKAIQKVVADGAGLPGEDWVFVSSKDA
DLTDTAQTRALFEKVQPTHVIHLAAMVGGLFRNIKYNLDFWRKNVHMNDN
VLHSAFEVGARKVVSCLSTCIFPDKTTYPIDETMIHNGPPHNSNFGYSYA
KRMIDVQNRAYFQQYGCTFTAVIPTNVFGPHDNFNIEDGHVLPGLIHKVH
LAKSSGSALTVWGTGNPRRQFIYSLDLAQLFIWVLREYNEVEPIILSVGE
EDEVSIKEAAEAVVEAMDFHGEVTFDTTKSDGQFKKTASNSKLRTYLPDF
RFTPFKQAVKETCAWFTDNYEQAR
Ligand information
Ligand IDNAP
InChIInChI=1S/C21H28N7O17P3/c22-17-12-19(25-7-24-17)28(8-26-12)21-16(44-46(33,34)35)14(30)11(43-21)6-41-48(38,39)45-47(36,37)40-5-10-13(29)15(31)20(42-10)27-3-1-2-9(4-27)18(23)32/h1-4,7-8,10-11,13-16,20-21,29-31H,5-6H2,(H7-,22,23,24,25,32,33,34,35,36,37,38,39)/t10-,11-,13-,14-,15-,16-,20-,21-/m1/s1
InChIKeyXJLXINKUBYWONI-NNYOXOHSSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0c1cc(c[n+](c1)C2C(C(C(O2)COP(=O)([O-])OP(=O)(O)OCC3C(C(C(O3)n4cnc5c4ncnc5N)OP(=O)(O)O)O)O)O)C(=O)N
CACTVS 3.341NC(=O)c1ccc[n+](c1)[CH]2O[CH](CO[P]([O-])(=O)O[P](O)(=O)OC[CH]3O[CH]([CH](O[P](O)(O)=O)[CH]3O)n4cnc5c(N)ncnc45)[CH](O)[CH]2O
CACTVS 3.341NC(=O)c1ccc[n+](c1)[C@@H]2O[C@H](CO[P]([O-])(=O)O[P@@](O)(=O)OC[C@H]3O[C@H]([C@H](O[P](O)(O)=O)[C@@H]3O)n4cnc5c(N)ncnc45)[C@@H](O)[C@H]2O
OpenEye OEToolkits 1.5.0c1cc(c[n+](c1)[C@H]2[C@@H]([C@@H]([C@H](O2)CO[P@@](=O)([O-])O[P@](=O)(O)OC[C@@H]3[C@H]([C@H]([C@@H](O3)n4cnc5c4ncnc5N)OP(=O)(O)O)O)O)O)C(=O)N
FormulaC21 H28 N7 O17 P3
NameNADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE;
2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE
ChEMBLCHEMBL295069
DrugBankDB03461
ZINC
PDB chain4bkp Chain B Residue 901 [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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PDB4bkp Crystal Structure of Human Gdp-L-Fucose Synthase with Bound Nadp
Resolution2.7 Å
Binding residue
(original residue number in PDB)		G14 S16 G17 L18 V19 S42 S43 D47 L48 L69 A71 M93 C112 L113 K147 V173 R320
Binding residue
(residue number reindexed from 1)		G18 S20 G21 L22 V23 S46 S47 D51 L52 L73 A75 M97 C116 L117 K151 V177 R324
Annotation score4
Enzymatic activity
Catalytic site (original residue number in PDB) S114 T115 C116 Y143 K147 H186
Catalytic site (residue number reindexed from 1) S118 T119 C120 Y147 K151 H190
Enzyme Commision number 1.1.1.271: GDP-L-fucose synthase.
Gene Ontology
Molecular Function
GO:0005515 protein binding
GO:0009055 electron transfer activity
GO:0016491 oxidoreductase activity
GO:0016853 isomerase activity
GO:0042356 GDP-4-dehydro-D-rhamnose reductase activity
GO:0042802 identical protein binding
GO:0047918 GDP-mannose 3,5-epimerase activity
GO:0050577 GDP-L-fucose synthase activity
Biological Process
GO:0007159 leukocyte cell-cell adhesion
GO:0009226 nucleotide-sugar biosynthetic process
GO:0010595 positive regulation of endothelial cell migration
GO:0019673 GDP-mannose metabolic process
GO:0042351 'de novo' GDP-L-fucose biosynthetic process
GO:1904906 positive regulation of endothelial cell-matrix adhesion via fibronectin
Cellular Component
GO:0005829 cytosol
GO:0070062 extracellular exosome

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:4bkp, PDBe:4bkp, PDBj:4bkp
PDBsum4bkp
PubMed
UniProtQ13630|FCL_HUMAN GDP-L-fucose synthase (Gene Name=GFUS)

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