Structure of PDB 6gpl Chain D Binding Site BS02

Receptor Information
>6gpl Chain D (length=341) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
RNVALITGITGQDGSYLAEFLLEKGYEVHGIVRRSSSFNTGRIEHLYNMK
LHYGDLTDSTCLVKIINEVKPTEIYNLGAQSHVKISFDLAEYTADVDGVG
TLRLLDAVKTCGLINSVKFYQASTSELYGKVQEIPQKETTPFYPRSPYGA
AKLYAYWIVVNFREAYNLFAVNGILFNHESPRRGANFVTRKISRSVAKIY
LGQLECFSLGNLDAKRDWGHAKDYVEAMWLMLQNDEPEDFVIATGEVHSV
REFVEKSFLHIGKTIVWEGKNENEVGRCKETGKVHVTVDLKYYRPTEVDF
LQGDCTKAKQKLNWKPRVAFDELVREMVHADVELMRTNPNA
Ligand information
Ligand IDF7E
InChIInChI=1S/C16H23N5O15P2/c1-4-7(22)9(24)11(26)15(33-4)35-38(30,31)36-37(28,29)32-2-5-8(23)10(25)14(34-5)21-3-18-6-12(21)19-16(17)20-13(6)27/h3-5,8-11,14-15,23-26H,2H2,1H3,(H,28,29)(H,30,31)(H3,17,19,20,27)/t4-,5-,8-,9+,10-,11+,14-,15-/m1/s1
InChIKeyPNHLMHWWFOPQLK-BKUUWRAGSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 2.0.6CC1C(=O)C(C(C(O1)OP(=O)(O)OP(=O)(O)OCC2C(C(C(O2)n3cnc4c3N=C(NC4=O)N)O)O)O)O
CACTVS 3.385C[CH]1O[CH](O[P](O)(=O)O[P](O)(=O)OC[CH]2O[CH]([CH](O)[CH]2O)n3cnc4C(=O)NC(=Nc34)N)[CH](O)[CH](O)C1=O
CACTVS 3.385C[C@H]1O[C@H](O[P](O)(=O)O[P](O)(=O)OC[C@H]2O[C@H]([C@H](O)[C@@H]2O)n3cnc4C(=O)NC(=Nc34)N)[C@@H](O)[C@@H](O)C1=O
OpenEye OEToolkits 2.0.6C[C@@H]1C(=O)[C@@H]([C@@H]([C@H](O1)OP(=O)(O)OP(=O)(O)OC[C@@H]2[C@H]([C@H]([C@@H](O2)n3cnc4c3N=C(NC4=O)N)O)O)O)O
FormulaC16 H23 N5 O15 P2
Name
ChEMBL
DrugBank
ZINCZINC000008217042
PDB chain6gpl Chain D Residue 3001 [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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PDB6gpl A Parsimonious Mechanism of Sugar Dehydration by Human GDP-Mannose-4,6-dehydratase.
Resolution1.76 Å
Binding residue
(original residue number in PDB)		S112 V114 T155 Y179 N208 R214 V219 K222 L240 G241 N242 R247 Y323 R325 E328
Binding residue
(residue number reindexed from 1)		S81 V83 T124 Y148 N177 R183 V188 K191 L209 G210 N211 R216 Y292 R294 E297
Annotation score4
Enzymatic activity
Catalytic site (original residue number in PDB) T155 S156 E157 Y179 K183
Catalytic site (residue number reindexed from 1) T124 S125 E126 Y148 K152
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:6gpl, PDBe:6gpl, PDBj:6gpl
PDBsum6gpl
PubMed30984471
UniProtO60547|GMDS_HUMAN GDP-mannose 4,6 dehydratase (Gene Name=GMDS)

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