Structure of PDB 4bc9 Chain A Binding Site BS02

Receptor Information
>4bc9 Chain A (length=555) Species: 10141 (Cavia porcellus) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
GIIPKKRQELMKWNGWGYNDSKFFLNKKGQLELTGKRYPLSGVALPTFKD
WIQNTFGINLDHKTDTPPSIVNEDFLHELKKTNISYSQEADDRVFRAHGH
CLHEIFLLREGMFERIPDIVLWPTCHDDVVKIVNLACKYNLCIIPIGGGT
SVSYGLMCPADETRTIISLDTSQMNRILWVDENNLTAHVEAGITGQELER
QLKESGYCTGHEPDSLEFSTVGGWISTRASGMKKNIYGNIEDLVVHMKVV
TPRGVIEKSCQGPRMSTGPDIHHFIMGSEGTLGVITEATIKIRPTPEYQK
YGSVAFPNFEQGVACLREIAKQRCAPASIRLMDNQQFQFGHALKPQVSSI
FTSGFDPNQLSVATLLFEGDREKVLQHEKQVYDIAAKFGGLAAGEDNGQR
GYLLTYVIAYMRDLGLEYYIIGESFETSAPWDRVVDLCRNVKERIRRECK
EKGVQFPPLSTCRVTQTYDAGACIYFYFAFNYRGISDPLAVFEQTEAAAR
EEILANGGSLSHHHGVGKLRKQWLKESISDVGFGMLKSVKDYVDPTNIFG
NRNLL
Ligand information
Ligand IDFAD
InChIInChI=1S/C27H33N9O15P2/c1-10-3-12-13(4-11(10)2)35(24-18(32-12)25(42)34-27(43)33-24)5-14(37)19(39)15(38)6-48-52(44,45)51-53(46,47)49-7-16-20(40)21(41)26(50-16)36-9-31-17-22(28)29-8-30-23(17)36/h3-4,8-9,14-16,19-21,26,37-41H,5-7H2,1-2H3,(H,44,45)(H,46,47)(H2,28,29,30)(H,34,42,43)/t14-,15+,16+,19-,20+,21+,26+/m0/s1
InChIKeyVWWQXMAJTJZDQX-UYBVJOGSSA-N
SMILES
SoftwareSMILES
CACTVS 3.341Cc1cc2N=C3C(=O)NC(=O)N=C3N(C[C@H](O)[C@H](O)[C@H](O)CO[P@](O)(=O)O[P@@](O)(=O)OC[C@H]4O[C@H]([C@H](O)[C@@H]4O)n5cnc6c(N)ncnc56)c2cc1C
OpenEye OEToolkits 1.5.0Cc1cc2c(cc1C)N(C3=NC(=O)NC(=O)C3=N2)CC(C(C(COP(=O)(O)OP(=O)(O)OCC4C(C(C(O4)n5cnc6c5ncnc6N)O)O)O)O)O
OpenEye OEToolkits 1.5.0Cc1cc2c(cc1C)N(C3=NC(=O)NC(=O)C3=N2)C[C@@H]([C@@H]([C@@H](CO[P@@](=O)(O)O[P@](=O)(O)OC[C@@H]4[C@H]([C@H]([C@@H](O4)n5cnc6c5ncnc6N)O)O)O)O)O
CACTVS 3.341Cc1cc2N=C3C(=O)NC(=O)N=C3N(C[CH](O)[CH](O)[CH](O)CO[P](O)(=O)O[P](O)(=O)OC[CH]4O[CH]([CH](O)[CH]4O)n5cnc6c(N)ncnc56)c2cc1C
ACDLabs 10.04O=C2C3=Nc1cc(c(cc1N(C3=NC(=O)N2)CC(O)C(O)C(O)COP(=O)(O)OP(=O)(O)OCC6OC(n5cnc4c(ncnc45)N)C(O)C6O)C)C
FormulaC27 H33 N9 O15 P2
NameFLAVIN-ADENINE DINUCLEOTIDE
ChEMBLCHEMBL1232653
DrugBankDB03147
ZINCZINC000008215434
PDB chain4bc9 Chain A Residue 999 [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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PDB4bc9 Precursor of Ether Phospholipids is Synthesized by a Flavoenzyme Through Covalent Catalysis.
Resolution2.41 Å
Binding residue
(original residue number in PDB)		P234 I235 G236 G237 G238 T239 S240 V241 G244 L245 P302 D303 S304 S308 T309 G312 W313 S315 T316 A318 S319 E368 V373 I374 H616
Binding residue
(residue number reindexed from 1)		P145 I146 G147 G148 G149 T150 S151 V152 G155 L156 P213 D214 S215 S219 T220 G223 W224 S226 T227 A229 S230 E279 V284 I285 H513
Annotation score1
Enzymatic activity
Enzyme Commision number 2.5.1.26: alkylglycerone-phosphate synthase.
Gene Ontology
Molecular Function
GO:0003824 catalytic activity
GO:0008609 alkylglycerone-phosphate synthase activity
GO:0016740 transferase activity
GO:0050660 flavin adenine dinucleotide binding
GO:0071949 FAD binding
Biological Process
GO:0006629 lipid metabolic process
GO:0008610 lipid biosynthetic process
GO:0008611 ether lipid biosynthetic process
Cellular Component
GO:0005777 peroxisome
GO:0005778 peroxisomal membrane
GO:0016020 membrane

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:4bc9, PDBe:4bc9, PDBj:4bc9
PDBsum4bc9
PubMed23112191
UniProtP97275|ADAS_CAVPO Alkyldihydroxyacetonephosphate synthase, peroxisomal (Gene Name=AGPS)

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