Structure of PDB 3f6e Chain X Binding Site BS01

Receptor Information
>3f6e Chain X (length=525) 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
QLKGSLQEALSAKGPVLIEVSTVSP
Ligand information
Ligand ID8PA
InChIInChI=1S/C20H25N5O8P2S/c1-13-18(7-9-32-35(30,31)33-34(27,28)29)36-20(17(26)6-5-15-4-3-8-22-10-15)25(13)12-16-11-23-14(2)24-19(16)21/h3-6,8,10-11,17,26H,7,9,12H2,1-2H3,(H4-,21,23,24,27,28,29,30,31)/p+1/b6-5+/t17-/m0/s1
InChIKeyHUCLASQGRJZNFE-RTRPANQVSA-O
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0Cc1c(sc([n+]1Cc2cnc(nc2N)C)[C@H](\C=C\c3cccnc3)O)CCO[P@](=O)(O)OP(=O)(O)O
CACTVS 3.341Cc1ncc(C[n+]2c(C)c(CCO[P@@](O)(=O)O[P](O)(O)=O)sc2[C@@H](O)\C=C\c3cccnc3)c(N)n1
ACDLabs 10.04O=P(O)(O)OP(=O)(O)OCCc1sc([n+](c1C)Cc2cnc(nc2N)C)C(O)\C=C\c3cccnc3
CACTVS 3.341Cc1ncc(C[n+]2c(C)c(CCO[P](O)(=O)O[P](O)(O)=O)sc2[CH](O)C=Cc3cccnc3)c(N)n1
OpenEye OEToolkits 1.5.0Cc1c(sc([n+]1Cc2cnc(nc2N)C)C(C=Cc3cccnc3)O)CCOP(=O)(O)OP(=O)(O)O
FormulaC20 H26 N5 O8 P2 S
Name3-[(4-amino-2-methylpyrimidin-5-yl)methyl]-5-(2-{[(S)-hydroxy(phosphonooxy)phosphoryl]oxy}ethyl)-2-[(1S,2E)-1-hydroxy-3-pyridin-3-ylprop-2-en-1-yl]-4-methyl-1,3-thiazol-3-ium
ChEMBL
DrugBank
ZINCZINC000058661274
PDB chain3f6e Chain X Residue 602 [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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PDB3f6e Detection and time course of formation of major thiamin diphosphate-bound covalent intermediates derived from a chromophoric substrate analogue on benzoylformate decarboxylase.
Resolution1.34 Å
Binding residue
(original residue number in PDB)		N23 P24 G25 S26 E47 H70
Binding residue
(residue number reindexed from 1)		N22 P23 G24 S25 E46 H69
Annotation score1
Binding affinityPDBbind-CN: -logKd/Ki=2.38,Kd=4.14mM
Enzymatic activity
Catalytic site (original residue number in PDB) G25 E47 L109 L110 T111 N112 G401 D428 N455 T457 Y458 A460 L461 S525
Catalytic site (residue number reindexed from 1) G24 E46 L108 L109 T110 N111 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:3f6e, PDBe:3f6e, PDBj:3f6e
PDBsum3f6e
PubMed19140682
UniProtP20906|MDLC_PSEPU Benzoylformate decarboxylase (Gene Name=mdlC)

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