Structure of PDB 5fb3 Chain F Binding Site BS01

Receptor Information
>5fb3 Chain F (length=337) Species: 410359 (Pyrobaculum calidifontis JCM 11548) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
KKVERFEVPRTIIFGPGALEKTPEVIPPSGRVLIITGKSSTRKYAERVAE
LLKQNCEIISYDQVELEKPGFDLVIGIGGGRPLDMAKVYSYIHKKPFVAI
PTSASHDGIASPYVSFSLTQRFSKYGKISSSPVAIIADTSIILSAPSRLL
KAGIGDLLGKIIAVRDWQLAHRLKGEEYSEYAAHLSLTSYKIAVGNAQKI
KNFIREEDVRVLVKALIGCGVAMGIAGSSRPCSGSEHLFAHAIEVRVEKE
DEVVHGELVALGTIIMAYLHGINWRRIKRIADIIGLPTSLRQANIDVDLA
LEALTTAHTLRPDRYTILGDGLSREAAKRALEDVELI
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 chain5fb3 Chain F Residue 402 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB5fb3 Unique coenzyme binding mode of hyperthermophilic archaeal sn-glycerol-1-phosphate dehydrogenase from Pyrobaculum calidifontis
Resolution2.45 Å
Binding residue
(original residue number in PDB)		G38 K39 S40 T42 G80 G81 R82 D85 T103 S106 H107 Y114 V115 S116 I142 S145 A146 L150 H256
Binding residue
(residue number reindexed from 1)		G37 K38 S39 T41 G79 G80 R81 D84 T102 S105 H106 Y113 V114 S115 I141 S144 A145 L149 H255
Annotation score4
Enzymatic activity
Catalytic site (original residue number in PDB) D157 H238 A241 H256
Catalytic site (residue number reindexed from 1) D156 H237 A240 H255
Enzyme Commision number 1.1.1.261: sn-glycerol-1-phosphate dehydrogenase.
Gene Ontology
Molecular Function
GO:0016491 oxidoreductase activity
GO:0016614 oxidoreductase activity, acting on CH-OH group of donors
GO:0046872 metal ion binding
GO:0050492 glycerol-1-phosphate dehydrogenase [NAD(P)+] activity
GO:0106357 glycerol-1-phosphate dehydrogenase (NAD+) activity
GO:0106358 glycerol-1-phosphate dehydrogenase (NADP+) activity
Biological Process
GO:0006650 glycerophospholipid metabolic process
GO:0008654 phospholipid biosynthetic process
Cellular Component
GO:0005737 cytoplasm

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:5fb3, PDBe:5fb3, PDBj:5fb3
PDBsum5fb3
PubMed27616573
UniProtA3MTM6|G1PDH_PYRCJ Glycerol-1-phosphate dehydrogenase [NAD(P)+] (Gene Name=egsA)

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