Structure of PDB 4bl5 Chain K Binding Site BS02

Receptor Information
>4bl5 Chain K (length=313) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MRILVTGGSGLVGKAIQKVVADGAGLPGEDWVFVSSKDADLTDTAQTRAL
FEKVQPTHVIHLAAMVGGLFRNIKYNLDFWRKNVHMNDNVLHSAFEVGAR
KVVSCLSTCIFPDKTTYPIDETMIHNGPPHNSNFGYSYAKRMIDVQNRAY
FQQYGCTFTAVIPTNVFGPHDNFNIEDGHVLPGLIHKVHLAKSSGSALTV
WGTGNPRRQFIYSLDLAQLFIWVLREYNEVEPIILSVGEEDEVSIKEAAE
AVVEAMDFHGEVTFDTTKSDGQFKKTASNSKLRTYLPDFRFTPFKQAVKE
TCAWFTDNYEQAR
Ligand information
Ligand IDGFB
InChIInChI=1S/C16H25N5O15P2/c1-4-7(22)9(24)11(26)15(33-4)35-38(30,31)36-37(28,29)32-2-5-8(23)10(25)14(34-5)21-3-18-6-12(21)19-16(17)20-13(6)27/h3-5,7-11,14-15,22-26H,2H2,1H3,(H,28,29)(H,30,31)(H3,17,19,20,27)/t4-,5+,7+,8+,9+,10+,11-,14+,15+/m0/s1
InChIKeyLQEBEXMHBLQMDB-JGQUBWHWSA-N
SMILES
SoftwareSMILES
ACDLabs 12.01O=C4NC(=Nc1c4ncn1C2OC(C(O)C2O)COP(=O)(OP(=O)(OC3OC(C(O)C(O)C3O)C)O)O)N
OpenEye OEToolkits 1.9.2CC1C(C(C(C(O1)OP(=O)(O)OP(=O)(O)OCC2C(C(C(O2)n3cnc4c3N=C(NC4=O)N)O)O)O)O)O
OpenEye OEToolkits 1.9.2C[C@H]1[C@H]([C@H]([C@@H]([C@H](O1)OP(=O)(O)OP(=O)(O)OC[C@@H]2[C@H]([C@H]([C@@H](O2)n3cnc4c3N=C(NC4=O)N)O)O)O)O)O
CACTVS 3.385C[C@@H]1O[C@H](O[P](O)(=O)O[P](O)(=O)OC[C@H]2O[C@H]([C@H](O)[C@@H]2O)n3cnc4C(=O)NC(=Nc34)N)[C@@H](O)[C@H](O)[C@@H]1O
CACTVS 3.385C[CH]1O[CH](O[P](O)(=O)O[P](O)(=O)OC[CH]2O[CH]([CH](O)[CH]2O)n3cnc4C(=O)NC(=Nc34)N)[CH](O)[CH](O)[CH]1O
FormulaC16 H25 N5 O15 P2
NameGUANOSINE-5'-DIPHOSPHATE-BETA-L-FUCOPYRANOSE
ChEMBLCHEMBL1229250
DrugBankDB18689
ZINCZINC000008551145
PDB chain4bl5 Chain K Residue 902 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
PDB4bl5 Crystal Structure of Human Gdp-L-Fucose Synthase with Bound Nadp and Product Gdp-L-Fucose
Resolution2.6 Å
Binding residue
(original residue number in PDB)		G74 G75 L76 C116 N140 Y143 N172 H186 V187 K194 W208 R215 I252 S276 D277 K282
Binding residue
(residue number reindexed from 1)		G67 G68 L69 C109 N133 Y136 N165 H179 V180 K187 W201 R208 I245 S269 D270 K275
Annotation score4
Enzymatic activity
Catalytic site (original residue number in PDB) S114 T115 C116 Y143 K147 H186
Catalytic site (residue number reindexed from 1) S107 T108 C109 Y136 K140 H179
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:4bl5, PDBe:4bl5, PDBj:4bl5
PDBsum4bl5
PubMed
UniProtQ13630|FCL_HUMAN GDP-L-fucose synthase (Gene Name=GFUS)

[Back to BioLiP]