Structure of PDB 3ud8 Chain A Binding Site BS02

Receptor Information
>3ud8 Chain A (length=129) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
KKPKLLYCSNGGHFLRILPDGTVDGTRDRSDQHIQLQLSAESVGEVYIKS
TETGQYLAMDTDGLLYGSQTPNEECLFLERLEENHYNTYISKKHAEKNWF
VGLKKNGSCKRGPRTHYGQKAILFLPLPV
Ligand information
Ligand IDGNX
InChIInChI=1S/C6H13NO11S2/c8-1-2-4(9)5(18-20(14,15)16)3(6(10)17-2)7-19(11,12)13/h2-10H,1H2,(H,11,12,13)(H,14,15,16)/t2-,3-,4-,5-,6+/m1/s1
InChIKeyAJBMJMMLWNUEAC-UKFBFLRUSA-N
SMILES
SoftwareSMILES
ACDLabs 12.01O=S(=O)(O)OC1C(O)C(OC(O)C1NS(=O)(=O)O)CO
OpenEye OEToolkits 1.7.2C(C1C(C(C(C(O1)O)NS(=O)(=O)O)OS(=O)(=O)O)O)O
OpenEye OEToolkits 1.7.2C([C@@H]1[C@H]([C@@H]([C@H]([C@H](O1)O)NS(=O)(=O)O)OS(=O)(=O)O)O)O
CACTVS 3.370OC[CH]1O[CH](O)[CH](N[S](O)(=O)=O)[CH](O[S](O)(=O)=O)[CH]1O
CACTVS 3.370OC[C@H]1O[C@H](O)[C@H](N[S](O)(=O)=O)[C@@H](O[S](O)(=O)=O)[C@@H]1O
FormulaC6 H13 N O11 S2
Name2-deoxy-3-O-sulfo-2-(sulfoamino)-alpha-D-glucopyranose;
2-deoxy-3-O-sulfo-2-(sulfoamino)-alpha-D-glucose;
2-deoxy-3-O-sulfo-2-(sulfoamino)-D-glucose;
2-deoxy-3-O-sulfo-2-(sulfoamino)-glucose
ChEMBL
DrugBank
ZINC
PDB chain3ud8 Chain D Residue 2 [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]
PDB3ud8 Divergent synthesis of 48 heparan sulfate-based disaccharides and probing the specific sugar-fibroblast growth factor-1 interaction
Resolution2.37 Å
Binding residue
(original residue number in PDB)		N18 K112 K113 K118
Binding residue
(residue number reindexed from 1)		N10 K104 K105 K110
Annotation score1
Binding affinityPDBbind-CN: -logKd/Ki=5.38,Kd=4.13uM
Enzymatic activity
Enzyme Commision number ?
Gene Ontology
Molecular Function
GO:0005104 fibroblast growth factor receptor binding
GO:0005178 integrin binding
GO:0005515 protein binding
GO:0008083 growth factor activity
GO:0008201 heparin binding
GO:0030544 Hsp70 protein binding
GO:0044548 S100 protein binding
Biological Process
GO:0001525 angiogenesis
GO:0001759 organ induction
GO:0007165 signal transduction
GO:0008284 positive regulation of cell population proliferation
GO:0008543 fibroblast growth factor receptor signaling pathway
GO:0009653 anatomical structure morphogenesis
GO:0009887 animal organ morphogenesis
GO:0010595 positive regulation of endothelial cell migration
GO:0010628 positive regulation of gene expression
GO:0030154 cell differentiation
GO:0030324 lung development
GO:0030334 regulation of cell migration
GO:0030335 positive regulation of cell migration
GO:0032148 activation of protein kinase B activity
GO:0034605 cellular response to heat
GO:0042060 wound healing
GO:0043406 positive regulation of MAP kinase activity
GO:0045542 positive regulation of cholesterol biosynthetic process
GO:0045766 positive regulation of angiogenesis
GO:0045944 positive regulation of transcription by RNA polymerase II
GO:0050673 epithelial cell proliferation
GO:0050679 positive regulation of epithelial cell proliferation
GO:0051781 positive regulation of cell division
GO:0060681 branch elongation involved in ureteric bud branching
GO:0070374 positive regulation of ERK1 and ERK2 cascade
GO:0072163 mesonephric epithelium development
GO:1901509 regulation of endothelial tube morphogenesis
GO:1902533 positive regulation of intracellular signal transduction
GO:1903672 positive regulation of sprouting angiogenesis
GO:2000347 positive regulation of hepatocyte proliferation
GO:2000544 regulation of endothelial cell chemotaxis to fibroblast growth factor
Cellular Component
GO:0005576 extracellular region
GO:0005615 extracellular space
GO:0005634 nucleus
GO:0005654 nucleoplasm
GO:0005737 cytoplasm
GO:0005829 cytosol
GO:0005938 cell cortex
GO:0031012 extracellular matrix

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:3ud8, PDBe:3ud8, PDBj:3ud8
PDBsum3ud8
PubMed23240683
UniProtP05230|FGF1_HUMAN Fibroblast growth factor 1 (Gene Name=FGF1)

[Back to BioLiP]