Structure of PDB 2z1m Chain D Binding Site BS01

Receptor Information
>2z1m Chain D (length=338) Species: 224324 (Aquifex aeolicus VF5) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
GKRALITGIRGQDGAYLAKLLLEKGYEVYGADRRSGEFASWRLKELGIEN
DVKIIHMDLLEFSNIIRTIEKVQPDEVYNLAAQSFVGVSFEQPILTAEVD
AIGVLRILEALRTVKPDTKFYQASTSEMFGKVQEIPQTEKTPFYPRSPYA
VAKLFGHWITVNYREAYNMFACSGILFNHESPLRGIEFVTRKITYSLARI
KYGLQDKLVLGNLNAKRDWGYAPEYVEAMWLMMQQPEPDDYVIATGETHT
VREFVEKAAKIAGFDIEWVGEGINEKGIDRNTGKVIVEVSEEFFRPAEVD
ILVGNPEKAMKKLGWKPRTTFDELVEIMMEADLKRVRD
Ligand information
Ligand IDNDP
InChIInChI=1S/C21H30N7O17P3/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/h1,3-4,7-8,10-11,13-16,20-21,29-31H,2,5-6H2,(H2,23,32)(H,36,37)(H,38,39)(H2,22,24,25)(H2,33,34,35)/t10-,11-,13-,14-,15-,16-,20-,21-/m1/s1
InChIKeyACFIXJIJDZMPPO-NNYOXOHSSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@](=O)(O)O[P@@](=O)(O)OC[C@@H]4[C@H]([C@H]([C@@H](O4)N5C=CCC(=C5)C(=O)N)O)O)O)OP(=O)(O)O)N
CACTVS 3.341NC(=O)C1=CN(C=CC1)[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)C1=CN(C=CC1)[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 1.5.0c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)OP(=O)(O)OCC4C(C(C(O4)N5C=CCC(=C5)C(=O)N)O)O)O)OP(=O)(O)O)N
FormulaC21 H30 N7 O17 P3
NameNADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
ChEMBLCHEMBL407009
DrugBankDB02338
ZINCZINC000008215411
PDB chain2z1m Chain D Residue 1101 [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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PDB2z1m Crystal Structure of GDP-D-Mannose Dehydratase from Aquifex aeolicus VF5
Resolution2.0 Å
Binding residue
(original residue number in PDB)		Q14 D34 R35 R36 D60 L61 L82 A83 A84 S86 A125 S126 T127 Y151 K155 L178 N180 H181 R186
Binding residue
(residue number reindexed from 1)		Q12 D32 R33 R34 D58 L59 L80 A81 A82 S84 A123 S124 T125 Y149 K153 L176 N178 H179 R184
Annotation score1
Enzymatic activity
Catalytic site (original residue number in PDB) T127 S128 E129 Y151 K155
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:0000166 nucleotide binding
GO:0008446 GDP-mannose 4,6-dehydratase activity
GO:0016829 lyase activity
GO:0070401 NADP+ binding
Biological Process
GO:0019673 GDP-mannose metabolic process
GO:0042351 'de novo' GDP-L-fucose biosynthetic process

View graph for
Molecular Function
View graph for
Biological Process
External links
PDB RCSB:2z1m, PDBe:2z1m, PDBj:2z1m
PDBsum2z1m
PubMed
UniProtO67175

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