Structure of PDB 4rgq Chain D Binding Site BS01

Receptor Information
>4rgq Chain D (length=331) Species: 243232 (Methanocaldococcus jannaschii DSM 2661) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MIIVTPRYTIIEDGAINKIEEILKKLNLKNPLVITGKNTKKYCRFFYDIV
YYDEILNNLKKYTAYDCVIGIGGGRSIDTGKYLAYKLGIPFISVPTTASN
DGIASPIVSIRQPSFMVDAPIAIIADTEIIKKSPRRLLSAGMGDIVSNIT
AVLDWKLAYKEKGEKYSESSAIFSKTIAKELISYVLNSDLSEYHNKLVKA
LVGSGIAIAIANSSRPASGSEHLFSHALDKLKEEYNLNINSLHGEQCGIG
TIMMSYLHEKENKKLSGLHEKIKMSLKKVDAPTTAKELGFDEDIIIEALT
MAHKIRNRWTILRDGLSREEARKLAEETGVI
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 chain4rgq Chain D Residue 401 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB4rgq Structure and Evolution of the Archaeal Lipid Synthesis Enzyme sn-Glycerol-1-phosphate Dehydrogenase.
Resolution2.23 Å
Binding residue
(original residue number in PDB)		G36 N38 T39 Y52 G78 D82 T100 T101 S103 N104 G106 I111 S113 S137 P138 L141 H247
Binding residue
(residue number reindexed from 1)		G36 N38 T39 Y52 G74 D78 T96 T97 S99 N100 G102 I107 S109 S133 P134 L137 H243
Annotation score4
Enzymatic activity
Catalytic site (original residue number in PDB) D148 H226 S229 H247
Catalytic site (residue number reindexed from 1) D144 H222 S225 H243
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:4rgq, PDBe:4rgq, PDBj:4rgq
PDBsum4rgq
PubMed26175150
UniProtQ58122|G1PDH_METJA Glycerol-1-phosphate dehydrogenase [NAD(P)+] (Gene Name=egsA)

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