Structure of PDB 2c3d Chain B Binding Site BS01

Receptor Information
>2c3d Chain B (length=522) Species: 78245 (Xanthobacter autotrophicus Py2) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
KVWNARNDHLTINQWATRIDEILEAPDGGEVIYNVDENDPREYDAIFIGG
GAAGRFGSAYLRAMGGRQLIVDRWPFLGGSCPHNACVPHHLFSDCAAELM
LARTFSGQYWFPDMTEKVVGIKEVVDLFRAGRNGPHGIMNFQSKEQLNLE
YILNCPAKVIDNHTVEAAGKVFKAKNLILAVGAGPGTLDVPGVNAKGVFD
HATLVEELDYEPGSTVVVVGGSKTAVEYGCFFNATGRRTVMLVRTEPLKL
IKDNETRAYVLDRMKEQGMEIISGSNVTRIEEDANGRVQAVVAMTPNGEM
RIETDFVFLGLGEQPRSAELAKILGLDLGPKGEVLVNEYLQTSVPNVYAV
GDLIGGPMEMFKARKSGCYAARNVMGEKISYTPKNYPDFLHTHYEVSFLG
MGEEEARAAGHEIVTIKMPPDTENGLNVALPASDRTMLYAFGKGTAHMSG
FQKIVIDAKTRKVLGAHHVGYGAKDAFQYLNVLIKQGLTVDELGDMDELF
LNPTHFIQLSRLRAGSKNLVSL
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 chain2c3d Chain B Residue 1524 [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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PDB2c3d Mechanistic Implications of the Structure of the Mixed-Disulfide Intermediate of the Disulfide Oxidoreductase, 2-Ketopropyl-Coenzyme M Oxidoreductase/Carboxylase.
Resolution2.15 Å
Binding residue
(original residue number in PDB)		G50 A53 A54 D73 R74 W75 G80 S81 A86 C87 H90 A158 A181 V182 H202 T225 G352 D353 M359 E360 M361
Binding residue
(residue number reindexed from 1)		G49 A52 A53 D72 R73 W74 G79 S80 A85 C86 H89 A157 A180 V181 H201 T224 G351 D352 M358 E359 M360
Annotation score2
Enzymatic activity
Catalytic site (original residue number in PDB) A53 L78 C82 C87 H90 F112 P113 H137 K224 E228 R365 F501 N503 I508
Catalytic site (residue number reindexed from 1) A52 L77 C81 C86 H89 F111 P112 H136 K223 E227 R364 F500 N502 I507
Enzyme Commision number 1.8.1.5: 2-oxopropyl-CoM reductase (carboxylating).
Gene Ontology
Molecular Function
GO:0003955 NAD(P)H dehydrogenase (quinone) activity
GO:0016491 oxidoreductase activity
GO:0050628 2-oxopropyl-CoM reductase (carboxylating) activity
GO:0050660 flavin adenine dinucleotide binding
Biological Process
GO:0042208 propylene catabolic process

View graph for
Molecular Function
View graph for
Biological Process
External links
PDB RCSB:2c3d, PDBe:2c3d, PDBj:2c3d
PDBsum2c3d
PubMed16388586
UniProtQ56839|XECC_XANP2 2-oxopropyl-CoM reductase, carboxylating (Gene Name=xecC)

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