Structure of PDB 4b8w Chain A Binding Site BS01

Receptor Information
>4b8w Chain A (length=319) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
NLYFQSMRILVTGGSGLVGKAIQKVVADGAGLPGEDWVFVSSKDADLTDT
AQTRALFEKVQPTHVIHLAAMVGGLFRNIKYNLDFWRKNVHMNDNVLHSA
FEVGARKVVSCLSTCIFPDKTTYPIDETMIHNGPPHNSNFGYSYAKRMID
VQNRAYFQQYGCTFTAVIPTNVFGPHDNFNIEDGHVLPGLIHKVHLAKSS
GSALTVWGTGNPRRQFIYSLDLAQLFIWVLREYNEVEPIILSVGEEDEVS
IKEAAEAVVEAMDFHGEVTFDTTKSDGQFKKTASNSKLRTYLPDFRFTPF
KQAVKETCAWFTDNYEQAR
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 chain4b8w Chain A Residue 900 [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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PDB4b8w Crystal Structure of Human Gdp-L-Fucose Synthase with Bound Nadp and Gdp, Tetragonal Crystal Form
Resolution2.75 Å
Binding residue
(original residue number in PDB)		G14 S16 G17 L18 V19 S42 S43 D47 L48 L69 A70 A71 V73 M93 C112 Y143 K147 P170 T171 V173 H186 R320
Binding residue
(residue number reindexed from 1)		G13 S15 G16 L17 V18 S41 S42 D46 L47 L68 A69 A70 V72 M92 C111 Y142 K146 P169 T170 V172 H185 R319
Annotation score4
Enzymatic activity
Catalytic site (original residue number in PDB) S114 T115 C116 Y143 K147 H186
Catalytic site (residue number reindexed from 1) S113 T114 C115 Y142 K146 H185
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

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:4b8w, PDBe:4b8w, PDBj:4b8w
PDBsum4b8w
PubMed
UniProtQ13630|FCL_HUMAN GDP-L-fucose synthase (Gene Name=GFUS)

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