Protein profile

PA4904

vanillate O-demethylase oxygenase

Genome: NC_002516.2

Gene: vanA PA4904 Structure source: AlphaFold UniProt Q9HUQ9
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Amino acids 351
Annotations 3
Features 16
PDB binders 7
Druggability 0.778

Overview

Basic information about this protein and its source genome.

Accession
PA4904
Assembly
Pseudomonas aeruginosa PAO1, complete genome
Gene
vanA PA4904
Status
annotated
Amino acids
351
Structure source
AlphaFold
GO
GO:0051537 Binding to a 2 iron, 2 sulfur (2Fe-2S) cluster; this cluster consists of two iron atoms, with two inorganic sulfur atoms found between the irons and acting as bridging ligands. GO:0005506 Binding to an iron (Fe) ion. GO:0016491 Catalysis of an oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced.

Target profile

Computed evidence for target prioritization.

Human off-target
No hit
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 0.778
Structure –
Pocket –

Sequence

Primary amino-acid sequence viewer.

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

3 GO

Gene Ontology (GO)

3
  • GO:0051537 Binding to a 2 iron, 2 sulfur (2Fe-2S) cluster; this cluster consists of two iron atoms, with two inorganic sulfur atoms found between the irons and acting as bridging ligands.
  • GO:0005506 Binding to an iron (Fe) ion.
  • GO:0016491 Catalysis of an oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced.

Sequence Features

Domain/signature hits from InterPro and related databases.

16 records
Show feature table
Start End DB Term Name
7 107 ProSiteProfiles PS51296 Rieske [2Fe-2S] iron-sulfur domain profile.
7 107 InterPro IPR017941 Rieske [2Fe-2S] iron-sulphur domain
133 337 CDD cd08878 RHO_alpha_C_DMO-like
3 110 SUPERFAMILY SSF50022 ISP domain
3 110 InterPro IPR036922 Rieske [2Fe-2S] iron-sulphur domain superfamily
117 343 SUPERFAMILY SSF55961 Bet v1-like
47 69 ProSitePatterns PS00570 Bacterial ring hydroxylating dioxygenases alpha-subunit signature.
47 69 InterPro IPR015881 Aromatic-ring-hydroxylating dioxygenase, 2Fe-2S-binding site
7 86 Pfam PF00355 Rieske [2Fe-2S] domain
7 86 InterPro IPR017941 Rieske [2Fe-2S] iron-sulphur domain
1 126 Gene3D G3DSA:2.102.10.10 -
1 126 InterPro IPR036922 Rieske [2Fe-2S] iron-sulphur domain superfamily
4 332 PANTHER PTHR21266 IRON-SULFUR DOMAIN CONTAINING PROTEIN
140 338 Pfam PF19112 Vanillate O-demethylase oxygenase C-terminal domain
140 338 InterPro IPR044043 Vanillate O-demethylase oxygenase-like, C-terminal catalytic domain
128 348 Gene3D G3DSA:3.90.380.10 -

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 PA4904
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
11 0.778
2 0.73

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.

57 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
30Q
4QDF
F1CMX0 457.7 Da LogP 5.33 TPSA 63.2 1 viol. ✓ Clean CCC(=O)NCCSC(=O)[C@@H](C)[C@H]1CC[C@@H]2[C@@]1(…
ASD
4QCK
P71875 286.4 Da LogP 4.09 TPSA 34.1 ✓ Ro5 ✓ Clean C[C@]12CCC(=O)C=C1CC[C@@H]3[C@@H]2CC[C@]4([C@H]…
D3M
3GB4
Q5S3I3 221.0 Da LogP 2.70 TPSA 46.5 ✓ Ro5 ✓ Clean COc1c(ccc(c1C(=O)O)Cl)Cl
FES
6WNC
C3RVP5 175.8 Da LogP 1.29 TPSA 0.0 ✓ Ro5 ✓ Clean S1[Fe]S[Fe]1
HXX
3GOB
Q5S3I3 207.0 Da LogP 2.40 TPSA 57.5 ✓ Ro5 ✓ Clean c1cc(c(c(c1Cl)C(=O)O)O)Cl
OXY
3GKE
Q5S3I3 32.0 Da LogP 0.07 TPSA 34.1 ✓ Ro5 ✓ Clean O=O
U5A
6WND
C3RVP5 267.3 Da LogP -1.72 TPSA 139.4 1 viol. ✓ Clean [H]/N=C\1/N[C@H]2[C@@H](N/C(=N/[H])/N3[C@]2(N1)…

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.