Structure of PDB 4b8z Chain B Binding Site BS02

Receptor Information
>4b8z Chain B (length=320) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
ENLYFQSMRILVTGGSGLVGKAIQKVVADGAGLPGEDWVFVSSKDADLTD
TAQTRALFEKVQPTHVIHLAAMVGGLFRNIKYNLDFWRKNVHMNDNVLHS
AFEVGARKVVSCLSTCIFPDKTTYPIDETMIHNGPPHNSNFGYSYAKRMI
DVQNRAYFQQYGCTFTAVIPTNVFGPHDNFNIEDGHVLPGLIHKVHLAKS
SGSALTVWGTGNPRRQFIYSLDLAQLFIWVLREYNEVEPIILSVGEEDEV
SIKEAAEAVVEAMDFHGEVTFDTTKSDGQFKKTASNSKLRTYLPDFRFTP
FKQAVKETCAWFTDNYEQAR
Ligand information
Ligand IDGDP
InChIInChI=1S/C10H15N5O11P2/c11-10-13-7-4(8(18)14-10)12-2-15(7)9-6(17)5(16)3(25-9)1-24-28(22,23)26-27(19,20)21/h2-3,5-6,9,16-17H,1H2,(H,22,23)(H2,19,20,21)(H3,11,13,14,18)/t3-,5-,6-,9-/m1/s1
InChIKeyQGWNDRXFNXRZMB-UUOKFMHZSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.7.6c1nc2c(n1C3C(C(C(O3)COP(=O)(O)OP(=O)(O)O)O)O)N=C(NC2=O)N
CACTVS 3.385NC1=Nc2n(cnc2C(=O)N1)[C@@H]3O[C@H](CO[P](O)(=O)O[P](O)(O)=O)[C@@H](O)[C@H]3O
CACTVS 3.385NC1=Nc2n(cnc2C(=O)N1)[CH]3O[CH](CO[P](O)(=O)O[P](O)(O)=O)[CH](O)[CH]3O
ACDLabs 12.01O=P(O)(O)OP(=O)(O)OCC3OC(n2cnc1c2N=C(N)NC1=O)C(O)C3O
OpenEye OEToolkits 1.7.6c1nc2c(n1[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@](=O)(O)OP(=O)(O)O)O)O)N=C(NC2=O)N
FormulaC10 H15 N5 O11 P2
NameGUANOSINE-5'-DIPHOSPHATE
ChEMBLCHEMBL384759
DrugBankDB04315
ZINCZINC000008215481
PDB chain4b8z 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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PDB4b8z Crystal Structure of Human Gdp-L-Fucose Synthase with Bound Nadp and Gdp, Rhombohedral Crystal Form
Resolution2.75 Å
Binding residue
(original residue number in PDB)		G75 L76 F77 H186 V187 K194 W208 R215 S276 D277 K282
Binding residue
(residue number reindexed from 1)		G75 L76 F77 H186 V187 K194 W208 R215 S276 D277 K282
Annotation score3
Enzymatic activity
Catalytic site (original residue number in PDB) S114 T115 C116 Y143 K147 H186
Catalytic site (residue number reindexed from 1) S114 T115 C116 Y143 K147 H186
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:4b8z, PDBe:4b8z, PDBj:4b8z
PDBsum4b8z
PubMed
UniProtQ13630|FCL_HUMAN GDP-L-fucose synthase (Gene Name=GFUS)

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