Structure of PDB 6gpj Chain D Binding Site BS01

Receptor Information
>6gpj Chain D (length=342) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MRNVALITGITGQDGSYLAEFLLEKGYEVHGIVRRSSSFNTGRIEHLYNM
KLHYGDLTDSTCLVKIINEVKPTEIYNLGAQSHVKISFDLAEYTADVDGV
GTLRLLDAVKTCGLINSVKFYQASTSELYGKVQEIPQKETTPFYPRSPYG
AAKLYAYWIVVNFREAYNLFAVNGILFNHESPRRGANFVTRKISRSVAKI
YLGQLECFSLGNLDAKRDWGHAKDYVEAMWLMLQNDEPEDFVIATGEVHS
VREFVEKSFLHIGKTIVWEGKNENEVGRCKETGKVHVTVDLKYYRPTEVD
FLQGDCTKAKQKLNWKPRVAFDELVREMVHADVELMRTNPNA
Ligand information
Ligand IDG4F
InChIInChI=1S/C16H24FN5O15P2/c17-6-4(1-23)35-15(11(27)9(6)25)36-39(31,32)37-38(29,30)33-2-5-8(24)10(26)14(34-5)22-3-19-7-12(22)20-16(18)21-13(7)28/h3-6,8-11,14-15,23-27H,1-2H2,(H,29,30)(H,31,32)(H3,18,20,21,28)/t4-,5-,6-,8-,9+,10-,11+,14-,15-/m1/s1
InChIKeyLDMYSLGOFVDHNN-YVXBHLEUSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 2.0.6c1nc2c(n1C3C(C(C(O3)COP(=O)(O)OP(=O)(O)OC4C(C(C(C(O4)CO)F)O)O)O)O)N=C(NC2=O)N
OpenEye OEToolkits 2.0.6c1nc2c(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)CO)F)O)O)O)O)N=C(NC2=O)N
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](CO)[C@@H](F)[C@H](O)[C@@H]4O)[C@@H](O)[C@H]3O
CACTVS 3.385NC1=Nc2n(cnc2C(=O)N1)[CH]3O[CH](CO[P](O)(=O)O[P](O)(=O)O[CH]4O[CH](CO)[CH](F)[CH](O)[CH]4O)[CH](O)[CH]3O
FormulaC16 H24 F N5 O15 P2
Name
ChEMBL
DrugBank
ZINC
PDB chain6gpj Chain D Residue 402 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB6gpj A Parsimonious Mechanism of Sugar Dehydration by Human GDP-Mannose-4,6-dehydratase.
Resolution1.94 Å
Binding residue
(original residue number in PDB)		S112 V114 T155 S156 E157 Y179 N208 R214 F218 V219 K222 G241 N242 R247 R325 E328
Binding residue
(residue number reindexed from 1)		S82 V84 T125 S126 E127 Y149 N178 R184 F188 V189 K192 G211 N212 R217 R295 E298
Annotation score3
Enzymatic activity
Catalytic site (original residue number in PDB) T155 S156 E157 Y179 K183
Catalytic site (residue number reindexed from 1) T125 S126 E127 Y149 K153
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
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Biological Process
View graph for
Cellular Component
External links
PDB RCSB:6gpj, PDBe:6gpj, PDBj:6gpj
PDBsum6gpj
PubMed30984471
UniProtO60547|GMDS_HUMAN GDP-mannose 4,6 dehydratase (Gene Name=GMDS)

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