Structure of PDB 4e5y Chain B Binding Site BS01

Receptor Information
>4e5y Chain B (length=309) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
SMRILVTGGSGLVGKAIQKVVADGAGEDWVFVSSKDADLTDTAQTRALFE
KVQPTHVIHLAAMVGGLFRNIKYNLDFWRKNVHMNDNVLHSAFEVGARKV
VSCLSTCIFPDKTTYPIDETMIHNGPPHNSNFGYSYAKRMIDVQNRAYFQ
QYGCTFTAVIPTNVFGPHDNFNIEDGHVLPGLIHKVHLAKSSGSLTVWGT
GNPRRQFIYSLDLAQLFIWVLREYNEVEPIILSVGEEDEVSIKEAAEAVV
EAMDFHGVTFDTTKSDQFKKTASNSKLRTYLPDFRFTPFKQAVKETCAWF
TDNYEQARK
Ligand information
Ligand IDNDP
InChIInChI=1S/C21H30N7O17P3/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/h1,3-4,7-8,10-11,13-16,20-21,29-31H,2,5-6H2,(H2,23,32)(H,36,37)(H,38,39)(H2,22,24,25)(H2,33,34,35)/t10-,11-,13-,14-,15-,16-,20-,21-/m1/s1
InChIKeyACFIXJIJDZMPPO-NNYOXOHSSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@](=O)(O)O[P@@](=O)(O)OC[C@@H]4[C@H]([C@H]([C@@H](O4)N5C=CCC(=C5)C(=O)N)O)O)O)OP(=O)(O)O)N
CACTVS 3.341NC(=O)C1=CN(C=CC1)[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)C1=CN(C=CC1)[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 1.5.0c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)OP(=O)(O)OCC4C(C(C(O4)N5C=CCC(=C5)C(=O)N)O)O)O)OP(=O)(O)O)N
FormulaC21 H30 N7 O17 P3
NameNADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
ChEMBLCHEMBL407009
DrugBankDB02338
ZINCZINC000008215411
PDB chain4e5y Chain B Residue 401 [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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PDB4e5y Structure of human FX protein, the key enzyme in the biosynthesis of GDP-L-fucose
Resolution2.37 Å
Binding residue
(original residue number in PDB)		G14 S16 G17 L18 V19 S42 S43 K44 A46 L48 L69 A71 C112 L113 S114 K147 P170 V173 R320
Binding residue
(residue number reindexed from 1)		G8 S10 G11 L12 V13 S33 S34 K35 A37 L39 L60 A62 C103 L104 S105 K138 P161 V164 R308
Annotation score4
Enzymatic activity
Catalytic site (original residue number in PDB) S114 T115 C116 Y143 K147 H186
Catalytic site (residue number reindexed from 1) S105 T106 C107 Y134 K138 H177
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:4e5y, PDBe:4e5y, PDBj:4e5y
PDBsum4e5y
PubMed
UniProtQ13630|FCL_HUMAN GDP-L-fucose synthase (Gene Name=GFUS)

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