Structure of PDB 5in4 Chain B Binding Site BS04

Receptor Information
>5in4 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 chain5in4 Chain B Residue 402 [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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PDB5in4 Facile Modulation of Antibody Fucosylation with Small Molecule Fucostatin Inhibitors and Cocrystal Structure with GDP-Mannose 4,6-Dehydratase.
Resolution1.6 Å
Binding residue
(original residue number in PDB)		G30 T32 G33 Q34 D35 R55 D86 L87 L108 G109 A110 S112 V127 A153 S154 T155 Y179 K183 L206 N208 H209 R214
Binding residue
(residue number reindexed from 1)		G9 T11 G12 Q13 D14 R34 D65 L66 L87 G88 A89 S91 V106 A132 S133 T134 Y158 K162 L185 N187 H188 R193
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

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Molecular Function
View graph for
Biological Process
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Cellular Component
External links
PDB RCSB:5in4, PDBe:5in4, PDBj:5in4
PDBsum5in4
PubMed27434622
UniProtO60547|GMDS_HUMAN GDP-mannose 4,6 dehydratase (Gene Name=GMDS)

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