Structure of PDB 5in4 Chain D Binding Site BS03

Receptor Information
>5in4 Chain D (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 ID6CK
InChIInChI=1S/C16H22F3N5O15P2/c17-16(18,19)10-7(27)6(26)9(29)14(37-10)38-41(33,34)39-40(31,32)35-1-3-5(25)8(28)13(36-3)24-2-21-4-11(24)22-15(20)23-12(4)30/h2-3,5-10,13-14,25-29H,1H2,(H,31,32)(H,33,34)(H3,20,22,23,30)/t3-,5-,6-,7+,8-,9+,10-,13-,14-/m1/s1
InChIKeyCBLFMUIUVZLPER-KLZHJQHWSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 2.0.4c1nc2c(n1[C@H]3[C@@H]([C@@H]([C@H](O3)COP(=O)(O)OP(=O)(O)O[C@@H]4[C@H]([C@@H]([C@@H]([C@@H](O4)C(F)(F)F)O)O)O)O)O)N=C(NC2=O)N
ACDLabs 12.01NC4=Nc3n(C1C(C(C(O1)COP(=O)(O)OP(O)(=O)OC2C(C(C(C(O2)C(F)(F)F)O)O)O)O)O)cnc3C(=O)N4
OpenEye OEToolkits 2.0.4c1nc2c(n1C3C(C(C(O3)COP(=O)(O)OP(=O)(O)OC4C(C(C(C(O4)C(F)(F)F)O)O)O)O)O)N=C(NC2=O)N
CACTVS 3.385NC1=Nc2n(cnc2C(=O)N1)[CH]3O[CH](CO[P](O)(=O)O[P](O)(=O)O[CH]4O[CH]([CH](O)[CH](O)[CH]4O)C(F)(F)F)[CH](O)[CH]3O
CACTVS 3.385NC1=Nc2n(cnc2C(=O)N1)[C@@H]3O[C@H](CO[P](O)(=O)O[P](O)(=O)O[C@H]4O[C@H]([C@@H](O)[C@@H](O)[C@@H]4O)C(F)(F)F)[C@@H](O)[C@H]3O
FormulaC16 H22 F3 N5 O15 P2
Name
ChEMBL
DrugBank
ZINCZINC000584904681
PDB chain5in4 Chain D 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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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)		F60 T62 Y69 H75 E77 L82 Y84
Binding residue
(residue number reindexed from 1)		F39 T41 Y48 H54 E56 L61 Y63
Annotation score3
Binding affinityMOAD: Kd=11uM
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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