Structure of PDB 2ji8 Chain A Binding Site BS04

Receptor Information
>2ji8 Chain A (length=559) Species: 847 (Oxalobacter formigenes) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
VELTDGFHVLIDALKMNDIDTMYGVVGIPITNLARMWQDDGQRFYSFRHE
QHAGYAASIAGYIEGKPGVCLTVSAPGFLNGVTSLAHATTNCFPMILLSG
SSEREIVDLQQGDYEEMDQMNVARPHCKASFRINSIKDIPIGIARAVRTA
VSGRPGGVYVDLPAKLFGQTISVEEANKLLFKPIDPAPAQIPAEDAIARA
ADLIKNAKRPVIMLGKGAAYAQCDDEIRALVEETGIPFLPMGMAKGLLPD
NHPQSAAATRAFALAQCDVCVLIGARLNWLMQHGKGKTWGDELKKYVQID
IQANEMDSNQPIAAPVVGDIKSAVSLLRKALKGAPKADAEWTGALKAKVD
GNKAKLAGKMTAETPSGMMNYSNSLGVVRDFMLANPDISLVNEGANALDN
TRMIVDMLKPRKRLDSGTWGVMGIGMGYCVAAAAVTGKPVIAVEGDSAFG
FSGMELETICRYNLPVTVIIMNNGGIYKGNEADPQPGVISCTRLTRGRYD
MMMEAFGGKGYVANTPAELKAALEEAVASGKPCLINAMIDPDAGVESGRI
KSLNVVSKV
Ligand information
Ligand IDFYN
InChIInChI=1S/C22H36N7O17P3S/c1-22(2,17(33)20(34)25-4-3-13(31)24-5-6-50-11-30)8-43-49(40,41)46-48(38,39)42-7-12-16(45-47(35,36)37)15(32)21(44-12)29-10-28-14-18(23)26-9-27-19(14)29/h9-12,15-17,21,32-33H,3-8H2,1-2H3,(H,24,31)(H,25,34)(H,38,39)(H,40,41)(H2,23,26,27)(H2,35,36,37)/t12-,15-,16-,17+,21-/m1/s1
InChIKeySXMOKYXNAPLNCW-GORZOVPNSA-N
SMILES
SoftwareSMILES
CACTVS 3.341CC(C)(CO[P](O)(=O)O[P](O)(=O)OC[CH]1O[CH]([CH](O)[CH]1O[P](O)(O)=O)n2cnc3c(N)ncnc23)[CH](O)C(=O)NCCC(=O)NCCSC=O
OpenEye OEToolkits 1.5.0CC(C)(CO[P@](=O)(O)O[P@](=O)(O)OC[C@@H]1[C@H]([C@H]([C@@H](O1)n2cnc3c2ncnc3N)O)OP(=O)(O)O)[C@H](C(=O)NCCC(=O)NCCSC=O)O
OpenEye OEToolkits 1.5.0CC(C)(COP(=O)(O)OP(=O)(O)OCC1C(C(C(O1)n2cnc3c2ncnc3N)O)OP(=O)(O)O)C(C(=O)NCCC(=O)NCCSC=O)O
CACTVS 3.341CC(C)(CO[P@@](O)(=O)O[P@@](O)(=O)OC[C@H]1O[C@H]([C@H](O)[C@@H]1O[P](O)(O)=O)n2cnc3c(N)ncnc23)[C@@H](O)C(=O)NCCC(=O)NCCSC=O
ACDLabs 10.04O=CSCCNC(=O)CCNC(=O)C(O)C(C)(C)COP(=O)(O)OP(=O)(O)OCC3OC(n2cnc1c(ncnc12)N)C(O)C3OP(=O)(O)O
FormulaC22 H36 N7 O17 P3 S
Name
ChEMBL
DrugBank
ZINCZINC000008551237
PDB chain2ji8 Chain A Residue 1569 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
PDB2ji8 Crystallographic Snapshots of Oxalyl-Coa Decarboxylase Give Insights Into Catalysis by Nonoxidative Thdp-Dependent Decarboxylases
Resolution2.15 Å
Binding residue
(original residue number in PDB)		A263 A264 T265 R266 A267 W285 L286 N358 L362 L404 R408 M409 S553 R555 I556
Binding residue
(residue number reindexed from 1)		A257 A258 T259 R260 A261 W279 L280 N352 L356 L398 R402 M403 S547 R549 I550
Annotation score4
Enzymatic activity
Catalytic site (original residue number in PDB) V31 G33 I34 P35 I36 E56 V79 Y120 E121 E122 A170 M287 G400 G426 M428 D452 N479 G481 I482 K484 G485 A488 P547
Catalytic site (residue number reindexed from 1) V25 G27 I28 P29 I30 E50 V73 Y114 E115 E116 A164 M281 G394 G420 M422 D446 N473 G475 I476 K478 G479 A482 P541
Enzyme Commision number 4.1.1.8: oxalyl-CoA decarboxylase.
Gene Ontology
Molecular Function
GO:0000166 nucleotide binding
GO:0000287 magnesium ion binding
GO:0003824 catalytic activity
GO:0008949 oxalyl-CoA decarboxylase activity
GO:0016831 carboxy-lyase activity
GO:0030976 thiamine pyrophosphate binding
GO:0042802 identical protein binding
GO:0043531 ADP binding
GO:0046872 metal ion binding
Biological Process
GO:0001561 fatty acid alpha-oxidation
GO:0019752 carboxylic acid metabolic process
GO:0033611 oxalate catabolic process

View graph for
Molecular Function
View graph for
Biological Process
External links
PDB RCSB:2ji8, PDBe:2ji8, PDBj:2ji8
PDBsum2ji8
PubMed17637344
UniProtP40149|OXC_OXAFO Oxalyl-CoA decarboxylase (Gene Name=oxc)

[Back to BioLiP]