Structure of PDB 4rfl Chain B Binding Site BS01

Receptor Information
>4rfl Chain B (length=332) Species: 243232 (Methanocaldococcus jannaschii DSM 2661) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
IIVTPRYTIIEDGAINKIEEILKKLNLKNPLVITGKNTKKYCRFFYDIVY
YDEILNNLELKKYTAYDCVIGIGGGRSIDTGKYLAYKLGIPFISVPTTAS
NDGIASPIVSIRQPSFMVDAPIAIIADTEIIKKSPRRLLSAGMGDIVSNI
TAVLDWKLAYKEKGEKYSESSAIFSKTIAKELISYVLNSDLSEYHNKLVK
ALVGSGIAIAIANSSRPASGSEHLFSHALDKLKEEYNLNINSLHGEQCGI
GTIMMSYLHEKENKKLSGLHEKIKMSLKKVDAPTTAKELGFDEDIIIEAL
TMAHKIRNRWTILRDGLSREEARKLAEETGVI
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 chain4rfl Chain B 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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PDB4rfl Structure and Evolution of the Archaeal Lipid Synthesis Enzyme sn-Glycerol-1-phosphate Dehydrogenase.
Resolution2.2 Å
Binding residue
(original residue number in PDB)		G36 N38 T39 Y52 G78 R79 T100 S103 N104 G106 S113 P138 L141 H247
Binding residue
(residue number reindexed from 1)		G35 N37 T38 Y51 G75 R76 T97 S100 N101 G103 S110 P135 L138 H244
Annotation score4
Enzymatic activity
Catalytic site (original residue number in PDB) D148 H226 S229 H247
Catalytic site (residue number reindexed from 1) D145 H223 S226 H244
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:4rfl, PDBe:4rfl, PDBj:4rfl
PDBsum4rfl
PubMed26175150
UniProtQ58122|G1PDH_METJA Glycerol-1-phosphate dehydrogenase [NAD(P)+] (Gene Name=egsA)

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