Structure of PDB 4rfl Chain C Binding Site BS01

Receptor Information
>4rfl Chain C (length=329) Species: 243232 (Methanocaldococcus jannaschii DSM 2661) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
IIVTPRYTIIEDGAINKIEEILKKLNLKNPLVITGKNTKKYCRFFYDIVY
YDEILNNKKYTAYDCVIGIGGGRSIDTGKYLAYKLGIPFISVPTTASNDG
IASPIVSIRQPSFMVDAPIAIIADTEIIKKSPRRLLSAGMGDIVSNITAV
LDWKLAYKEKGEKYSESSAIFSKTIAKELISYVLNSDLSEYHNKLVKALV
GSGIAIAIANSSRPASGSEHLFSHALDKLKEEYNLNINSLHGEQCGIGTI
MMSYLHEKENKKLSGLHEKIKMSLKKVDAPTTAKELGFDEDIIIEALTMA
HKIRNRWTILRDGLSREEARKLAEETGVI
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 C 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 K37 N38 T39 Y42 Y52 G77 G78 R79 T100 S103 N104 G106 I111 S113 S137 P138 H247
Binding residue
(residue number reindexed from 1)		G35 K36 N37 T38 Y41 Y51 G71 G72 R73 T94 S97 N98 G100 I105 S107 S131 P132 H241
Annotation score4
Enzymatic activity
Catalytic site (original residue number in PDB) D148 H226 S229 H247
Catalytic site (residue number reindexed from 1) D142 H220 S223 H241
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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