Structure of PDB 5in5 Chain B Binding Site BS01

Receptor Information
>5in5 Chain B (length=351) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
GRNVALITGITGQDGSYLAEFLLEKGYEVHGIVRRSSSFNTGRIEHLYKN
PQAHIEGNMKLHYGDLTDSTCLVKIINEVKPTEIYNLGAQSHVKISFDLA
EYTADVDGVGTLRLLDAVKTCGLINSVKFYQASTSELYGKVQEIPQKETT
PFYPRSPYGAAKLYAYWIVVNFREAYNLFAVNGILFNHESPRRGANFVTR
KISRSVAKIYLGQLECFSLGNLDAKRDWGHAKDYVEAMWLMLQNDEPEDF
VIATGEVHSVREFVEKSFLHIGKTIVWEGKNENEVGRCKETGKVHVTVDL
KYYRPTEVDFLQGDCTKAKQKLNWKPRVAFDELVREMVHADVELMRTNPN
A
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 chain5in5 Chain A Residue 1001 [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]
PDB5in5 Facile Modulation of Antibody Fucosylation with Small Molecule Fucostatin Inhibitors and Cocrystal Structure with GDP-Mannose 4,6-Dehydratase.
Resolution1.9 Å
Binding residue
(original residue number in PDB)		R56 S57 S58
Binding residue
(residue number reindexed from 1)		R35 S36 S37
Annotation score1
Enzymatic activity
Catalytic site (original residue number in PDB) T155 S156 E157 Y179 K183
Catalytic site (residue number reindexed from 1) T134 S135 E136 Y158 K162
Enzyme Commision number 4.2.1.47: GDP-mannose 4,6-dehydratase.
Gene Ontology
Molecular Function
GO:0005515 protein binding
GO:0008446 GDP-mannose 4,6-dehydratase activity
GO:0016829 lyase activity
GO:0042802 identical protein binding
GO:0070401 NADP+ binding
Biological Process
GO:0007219 Notch signaling pathway
GO:0019673 GDP-mannose metabolic process
GO:0042350 GDP-L-fucose biosynthetic process
GO:0042351 'de novo' GDP-L-fucose biosynthetic process
Cellular Component
GO:0005737 cytoplasm
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:5in5, PDBe:5in5, PDBj:5in5
PDBsum5in5
PubMed27434622
UniProtO60547|GMDS_HUMAN GDP-mannose 4,6 dehydratase (Gene Name=GMDS)

[Back to BioLiP]