Structure of PDB 3fsj Chain X Binding Site BS01

Receptor Information
>3fsj Chain X (length=524) Species: 303 (Pseudomonas putida) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
ASVHGTTYELLRRQGIDTVFGNPGSNELPFLKDFPEDFRYILALQEACVV
GIADGYAQASRKPAFINLHSAAGTGNAMGALSNAWNSHSPLIVTAGQQTR
AMIGVEALLTNVDAANLPRPLVKWSYEPASAAEVPHAMSRAIHMASMAPQ
GPVYLSVPYDDWDKDADPQSHHLFDRHVSSSVRLNDQDLDILVKALNSAS
NPAIVLGPDVDAANANADCVMLAERLKAPVWVAPSAPRCPFPTRHPCFRG
LMPAGIAAISQLLEGHDVVLVIGAPVFRYHQYDPGQYLKPGTRLISVTCD
PLEAARAPMGDAIVADIGAMASALANLVEESSRQLPTAAPEPAKVDQDAG
RLHPETVFDTLNDMAPENAIYLNESTSTTAQMWQRLNMRNPGSYYFCAAG
GLGFALPAAIGVQLAEPERQVIAVIGDGSANYSISALWTAAQYNIPTIFV
IMNNGTYGALRWFAGVLEAENVPGLDVPGIDFRALAKGYGVQALKADNLE
QLKGSLQEALSAKGPVLIEVSTVS
Ligand information
Ligand IDD7K
InChIInChI=1S/C20H27N4O11P3S/c1-13-17(9-10-34-38(31,32)35-37(28,29)30)39-19(24(13)12-15-11-22-14(2)23-18(15)21)20(25,36(26,27)33-3)16-7-5-4-6-8-16/h4-8,11,25H,9-10,12H2,1-3H3,(H5-,21,22,23,26,27,28,29,30,31,32)/p+1/t20-/m0/s1
InChIKeyNEEQBMRCDKRNBV-FQEVSTJZSA-O
SMILES
SoftwareSMILES
ACDLabs 10.04O=P(O)(OP(=O)(O)O)OCCc1sc([n+](c1C)Cc2cnc(nc2N)C)C(O)(c3ccccc3)P(=O)(OC)O
OpenEye OEToolkits 1.5.0Cc1c(sc([n+]1Cc2cnc(nc2N)C)C(c3ccccc3)(O)P(=O)(O)OC)CCOP(=O)(O)OP(=O)(O)O
OpenEye OEToolkits 1.5.0Cc1c(sc([n+]1Cc2cnc(nc2N)C)[C@@](c3ccccc3)(O)[P@@](=O)(O)OC)CCO[P@@](=O)(O)OP(=O)(O)O
CACTVS 3.341CO[P](O)(=O)[C](O)(c1ccccc1)c2sc(CCO[P](O)(=O)O[P](O)(O)=O)c(C)[n+]2Cc3cnc(C)nc3N
CACTVS 3.341CO[P@@](O)(=O)[C@@](O)(c1ccccc1)c2sc(CCO[P@](O)(=O)O[P](O)(O)=O)c(C)[n+]2Cc3cnc(C)nc3N
FormulaC20 H28 N4 O11 P3 S
Name3-[(4-amino-2-methylpyrimidin-5-yl)methyl]-2-{(S)-hydroxy[(R)-hydroxy(methoxy)phosphoryl]phenylmethyl}-5-(2-{[(R)-hydroxy(phosphonooxy)phosphoryl]oxy}ethyl)-4-methyl-1,3-thiazol-3-ium
ChEMBL
DrugBank
ZINCZINC000058661176
PDB chain3fsj Chain X Residue 601 [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]
PDB3fsj Snapshot of a reaction intermediate: analysis of benzoylformate decarboxylase in complex with a benzoylphosphonate inhibitor.
Resolution1.37 Å
Binding residue
(original residue number in PDB)		H281 T377 S378 F397 G401 L403 G427 D428 G429 S430 Y433 T457 Y458 G459 A460 L461 F464 V524 S525
Binding residue
(residue number reindexed from 1)		H280 T376 S377 F396 G400 L402 G426 D427 G428 S429 Y432 T456 Y457 G458 A459 L460 F463 V523 S524
Annotation score1
Binding affinityMOAD: Kd=0.113mM
PDBbind-CN: -logKd/Ki=3.95,Kd=0.113mM
Enzymatic activity
Catalytic site (original residue number in PDB) G25 S26 E28 E47 H70 L109 L110 T111 N112 H281 G401 D428 N455 T457 Y458 A460 L461 S525
Catalytic site (residue number reindexed from 1) G24 S25 E27 E46 H69 L108 L109 T110 N111 H280 G400 D427 N454 T456 Y457 A459 L460 S524
Enzyme Commision number 4.1.1.7: benzoylformate decarboxylase.
Gene Ontology
Molecular Function
GO:0000287 magnesium ion binding
GO:0003824 catalytic activity
GO:0003984 acetolactate synthase activity
GO:0016831 carboxy-lyase activity
GO:0030976 thiamine pyrophosphate binding
GO:0046872 metal ion binding
GO:0050660 flavin adenine dinucleotide binding
GO:0050695 benzoylformate decarboxylase activity
Biological Process
GO:0009056 catabolic process
GO:0018924 mandelate metabolic process
GO:0019596 mandelate catabolic process
GO:0019752 carboxylic acid metabolic process

View graph for
Molecular Function
View graph for
Biological Process
External links
PDB RCSB:3fsj, PDBe:3fsj, PDBj:3fsj
PDBsum3fsj
PubMed19320438
UniProtP20906|MDLC_PSEPU Benzoylformate decarboxylase (Gene Name=mdlC)

[Back to BioLiP]