Protein profile

PA4901

benzoylformate decarboxylase

Genome: NC_002516.2

Gene: PA4901 mdlC Structure source: AlphaFold UniProt Q9HUR2
Amino acids 528
Annotations 8
Features 21
PDB binders 29
Druggability 0.839

Overview

Basic information about this protein and its source genome.

Accession
PA4901
Gene
PA4901 mdlC
Status
annotated
Amino acids
528
Structure source
AlphaFold

Target profile

Computed evidence for target prioritization.

Human off-target
hit
Human identity (%)
26.974
Human E-value
7.5e-06
Gut microbiome off-target
hit
Essential (DEG)
N
Localization
Cytoplasmic

Selected Druggability evidence

Selected Druggability is the FPocket score chosen for ranking using the curated structure priority. The 3D viewer may show a different loaded structure, so its visible pockets can differ.

FPocket 0.839
Structure
Pocket

Sequence

Primary amino-acid sequence viewer.

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 7 GO

Enzyme Commission (EC)

1

Gene Ontology (GO)

7
  • GO:0003984 Catalysis of the reaction: H+ + 2 pyruvate = (2S)-2-acetolactate + CO2. Can also convert 2-oxobutanoate and pyruvate to (S)-2-ethyl-2-hydroxy-3-oxobutanoate.
  • GO:0050695 Catalysis of the reaction: benzoylformate = benzaldehyde + CO2.
  • GO:0050660 Binding to FAD, flavin-adenine dinucleotide, the coenzyme or the prosthetic group of various flavoprotein oxidoreductase enzymes, in either the oxidized form, FAD, or the reduced form, FADH2.
  • GO:0000287 Binding to a magnesium (Mg) ion.
  • GO:0030976 Binding to thiamine pyrophosphate, the diphosphoric ester of thiamine. Acts as a coenzyme of several (de)carboxylases, transketolases, and alpha-oxoacid dehydrogenases.
  • GO:0019596 The chemical reactions and pathways resulting in the breakdown of mandelate, the anion of mandelic acid. Mandelic acid (alpha-hydroxybenzeneacetic acid) is an 8-carbon alpha-hydroxy acid (AHA) that is used in organic chemistry and as a urinary antiseptic.
  • GO:0003824 Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.

Sequence Features

Domain/signature hits from InterPro and related databases.

21 records
Show feature table
Start End DB Term Name
1 178 Gene3D G3DSA:3.40.50.970 -
183 341 Gene3D G3DSA:3.40.50.1220 -
4 168 Pfam PF02776 Thiamine pyrophosphate enzyme, N-terminal TPP binding domain
4 168 InterPro IPR012001 Thiamine pyrophosphate enzyme, N-terminal TPP-binding domain
411 430 ProSitePatterns PS00187 Thiamine pyrophosphate enzymes signature.
411 430 InterPro IPR000399 TPP-binding enzyme, conserved site
351 525 SUPERFAMILY SSF52518 Thiamin diphosphate-binding fold (THDP-binding)
351 525 InterPro IPR029061 Thiamin diphosphate-binding fold
345 525 Gene3D G3DSA:3.40.50.970 -
185 341 SUPERFAMILY SSF52467 DHS-like NAD/FAD-binding domain
185 341 InterPro IPR029035 DHS-like NAD/FAD-binding domain superfamily
353 523 CDD cd02002 TPP_BFDC
382 521 Pfam PF02775 Thiamine pyrophosphate enzyme, C-terminal TPP binding domain
382 521 InterPro IPR011766 Thiamine pyrophosphate enzyme, TPP-binding
9 160 CDD cd07035 TPP_PYR_POX_like
4 524 PANTHER PTHR18968 THIAMINE PYROPHOSPHATE ENZYMES
4 524 InterPro IPR045229 Thiamine pyrophosphate enzyme
192 325 Pfam PF00205 Thiamine pyrophosphate enzyme, central domain
192 325 InterPro IPR012000 Thiamine pyrophosphate enzyme, central domain
4 170 SUPERFAMILY SSF52518 Thiamin diphosphate-binding fold (THDP-binding)
4 170 InterPro IPR029061 Thiamin diphosphate-binding fold

3D Structure

Selected loaded structure. Experimental PDB entries may cover only a portion of the sequence; predicted models typically cover the full protein.

3D visualization script Full viewer

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Structural evidence

0 + 1

Experimental PDB entries and predicted models. Click Switch to display a different structure in the viewer.

Entry Method Resolution Chain Coverage Links Status
AlphaFold PA4901
AlphaFold full sequence Viewing
Pocket details FPocket · P2Rank — toggle visibility and zoom from here, or open full viewer

Pockets (FPOCKET)

Showing top-ranked FPocket candidates by druggability. Druggability is color-coded: high (0.7 or higher), medium (0.4 to 0.69), low (below 0.4).

FPOCKET Sticks Spheres Surfaces Druggability Labels Zoom Positions
1 0.839

Ligand evidence

Ligands grouped by evidence source. PDB ligands keep the source crystal visible, and loaded crystals can be opened directly in the structure viewer.

85 records

Structural evidence inferred from similar proteins. The source crystal indicates where the ligand was observed; the UniProt column identifies the homologous protein carrying that ligand.

Show only:
Ligand Source crystal UniProt (homolog) MW · LogP · TPSA Lipinski PAINS SMILES
1MM P07342 381.4 Da LogP 0.49 TPSA 149.5 ✓ Ro5 ✓ Clean Cc1nc(nc(n1)OC)NC(=O)NS(=O)(=O)c2ccccc2C(=O)OC
1SM A0A1D8PJF9 364.4 Da LogP 1.39 TPSA 127.3 ✓ Ro5 ✓ Clean Cc1cc(nc(n1)NC(=O)NS(=O)(=O)c2ccccc2C(=O)OC)C
60G A0A1D8PJF9 410.4 Da LogP 0.93 TPSA 145.8 ✓ Ro5 ✓ Clean COc1cc(nc(n1)NC(=O)NS(=O)(=O)Cc2ccccc2C(=O)OC)OC
6R4 A0A1D8PJF9 398.4 Da LogP 0.10 TPSA 138.6 ✓ Ro5 ✓ Clean CCCOC1=NN(C(=O)N1C)C(=O)NS(=O)(=O)c2ccccc2C(=O)…
8PA P20906 558.5 Da LogP 1.98 TPSA 202.1 1 viol. ✓ Clean Cc1c(sc([n+]1Cc2cnc(nc2N)C)[C@H](\C=C\c3cccnc3)…
AUJ P07342 Cc1ncc(c(n1)N)C[N]2=C(SC(=C2C)CCOP(=O)(O)OP(=O)…
AYD P07342 382.3 Da LogP 0.98 TPSA 177.1 ✓ Ro5 ✓ Clean Cc1ncc(c(n1)N)CN/C(=C/CCO[P@@](=O)(O)OP(=O)(O)O…
CO2 P07342 44.0 Da LogP -0.58 TPSA 34.1 ✓ Ro5 ✓ Clean C(=O)=O
D7K P20906 625.5 Da LogP 1.87 TPSA 235.7 3 viol. ✓ Clean Cc1c(sc([n+]1Cc2cnc(nc2N)C)[C@@](c3ccccc3)(O)[P…
DTT P07342 154.3 Da LogP -0.43 TPSA 40.5 ✓ Ro5 ✓ Clean C([C@@H]([C@H](CS)O)O)S
F50 P07342 76.1 Da LogP 0.02 TPSA 46.5 ✓ Ro5 ✓ Clean CC(=O)OO
G87 A0A1D8PJF9 418.3 Da LogP 2.56 TPSA 107.7 ✓ Ro5 ✓ Clean Cc1ccc(c(c1Cl)NS(=O)(=O)c2nc3nc(cc(n3n2)OC)OC)Cl
G8A A0A1D8PJF9 506.3 Da LogP 1.78 TPSA 136.6 1 viol. ✓ Clean CCOC(=O)c1ccccc1S(=O)(=O)NC(=O)Nc2nc(cc(n2)I)OC
G8G A0A1D8PJF9 442.3 Da LogP 1.10 TPSA 185.4 ✓ Ro5 ✓ Clean Cc1ncc(c(n1)N)CN(C=O)/C(=C(/CCOP(=O)(O)OP(=O)(O…
H4V A0A1D8PJF9 492.3 Da LogP 1.39 TPSA 136.6 ✓ Ro5 ✓ Clean COc1cc(nc(n1)NC(=O)NS(=O)(=O)c2ccccc2C(=O)OC)I
HTL P07342 467.4 Da LogP 1.04 TPSA 186.0 ✓ Ro5 ✓ Clean Cc1c(sc([n+]1Cc2cnc(nc2N)C)C(=O)C)CCO[P@@](=O)(…
NSP P07342 138.2 Da LogP -0.17 TPSA 77.8 ✓ Ro5 ✓ Clean Cc1ncc(c(n1)N)CN
OXY P07342 32.0 Da LogP 0.07 TPSA 34.1 ✓ Ro5 ✓ Clean O=O
P22 P07342 206.0 Da LogP 0.23 TPSA 113.3 ✓ Ro5 ✓ Clean CCO[P@](=O)(O)OP(=O)(O)O
P23 P07342 220.1 Da LogP 0.62 TPSA 113.3 ✓ Ro5 ✓ Clean CCCO[P@@](=O)(O)OP(=O)(O)O
P25 P07342 248.1 Da LogP 1.40 TPSA 113.3 ✓ Ro5 ✓ Clean CCCCCO[P@@](=O)(O)OP(=O)(O)O
PXD P07342 483.4 Da LogP 2.61 TPSA 116.9 ✓ Ro5 ✓ Clean COc1cnc(n2c1nc(n2)NS(=O)(=O)c3c(cccc3OCC(F)F)C(…
PYD P07342 123.2 Da LogP 0.68 TPSA 51.8 ✓ Ro5 ✓ Clean Cc1cnc(nc1N)C
PYR P07342 88.1 Da LogP -0.34 TPSA 54.4 ✓ Ro5 ✓ Clean CC(=O)C(=O)O
RMN P20906 152.1 Da LogP 0.80 TPSA 57.5 ✓ Ro5 ✓ Clean c1ccc(cc1)[C@H](C(=O)O)O
TP9 P07342 412.3 Da LogP -0.03 TPSA 182.8 1 viol. ✓ Clean Cc1ncc(c(n1)N)CN/C(=C(/CCO[P@](=O)([O-])O[P@@](…
TZD P20906 440.3 Da LogP 0.72 TPSA 187.1 ✓ Ro5 ✓ Clean Cc1ncc(c(n1)N)CN2C(=C(SC2=O)CCO[P@@](=O)(O)OP(=…
YF3 P07342 212.3 Da LogP 0.78 TPSA 63.8 ✓ Ro5 ✓ Clean Cc1ncc(c(n1)N)CNC(C)CS
YF4 P07342 180.3 Da LogP 0.82 TPSA 55.0 ✓ Ro5 ✓ Clean CCN(C)Cc1cnc(nc1N)C

PDB and ChEMBL records on this protein are shown in full. ChEMBL records from similar proteins are capped at the top 100 per protein (by pchembl) and ZINC at the top 50 (Tanimoto ≥ 0.5). ADME columns are descriptor-based screening flags, not experimental toxicity results.