Protein profile

VK055_2617

4-hydroxybenzoate 3-monooxygenase

Genome: KpATCC43816

Gene: pobA AIK81211.1 Structure source: AlphaFold + ColabFold UniProt A0A0H3GIS2

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Amino acids 394

Annotations 5

Features 16

PDB binders 11

Druggability 0.611

Overview

Basic information about this protein and its source genome.

Accession: VK055_2617
Assembly: Klebsiella pneumoniae subsp. pneumoniae strain ATCC 43816 KPPR1, complete genome
Gene: pobA AIK81211.1
Status: annotated
Amino acids: 394
Structure source: AlphaFold + ColabFold

1.14.13.2

GO:0071949 Binding to the oxidized form, FAD, of flavin-adenine dinucleotide, the coenzyme or the prosthetic group of various flavoprotein oxidoreductase enzymes. 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:0018659 Catalysis of the reaction: 4-hydroxybenzoate + NADPH + H+ + O2 = protocatechuate + NADP+ + H2O. GO:0043639 The chemical reactions and pathways resulting in the breakdown of benzoate, the anion of benzoic acid (benzenecarboxylic acid), a fungistatic compound widely used as a food preservative; it is conjugated to glycine in the liver and excreted as hippuric acid.

Target profile

Computed evidence for target prioritization.

Human off-target: No hit
Human identity (%): 0.0
Gut microbiome off-target: hit
Essential (DEG): N
DEG identity (%): 26.556
Localization: Cytoplasmic
ColabFold pLDDT: 97.25

Selected Druggability evidence

AlphaFold / UniProt model

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 0.611

Structure A0A0H3GIS2

Pocket Pocket 9

P2Rank 0.92

Structure A0A0H3GIS2

Pocket Pocket 1

ColabFold model

FPocket 0.719 · Pocket 2

P2Rank 0.94 · Pocket 1

Core conservation Conserved core gene

Roary core

CoreCruncher core

Gut microbiome 48 / 4744 genomes with a hit

Normalized 0.01

Sequence

Primary amino-acid sequence viewer.

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 4 GO

Enzyme Commission (EC)

1.14.13.2

Gene Ontology (GO)

GO:0071949 Binding to the oxidized form, FAD, of flavin-adenine dinucleotide, the coenzyme or the prosthetic group of various flavoprotein oxidoreductase enzymes.
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:0018659 Catalysis of the reaction: 4-hydroxybenzoate + NADPH + H+ + O2 = protocatechuate + NADP+ + H2O.
GO:0043639 The chemical reactions and pathways resulting in the breakdown of benzoate, the anion of benzoic acid (benzenecarboxylic acid), a fungistatic compound widely used as a food preservative; it is conjugated to glycine in the liver and excreted as hippuric acid.

Sequence Features

Domain/signature hits from InterPro and related databases.

16 records

Show feature table

Start	End	DB	Term	Name
2	351	Gene3D	G3DSA:3.50.50.60	-
2	351	InterPro	IPR036188	FAD/NAD(P)-binding domain superfamily
1	388	SUPERFAMILY	SSF51905	FAD/NAD(P)-binding domain
1	388	InterPro	IPR036188	FAD/NAD(P)-binding domain superfamily
2	342	Pfam	PF01494	FAD binding domain
2	342	InterPro	IPR002938	FAD-binding domain
2	329	PANTHER	PTHR43004	TRK SYSTEM POTASSIUM UPTAKE PROTEIN
1	390	NCBIfam	TIGR02360	4-hydroxybenzoate 3-monooxygenase
1	390	InterPro	IPR012733	4-hydroxybenzoate 3-monooxygenase
175	275	SUPERFAMILY	SSF54373	FAD-linked reductases, C-terminal domain
73	388	Gene3D	G3DSA:3.30.9.10	-
293	309	PRINTS	PR00420	Aromatic-ring hydroxylase (flavoprotein monooxygenase) signature
310	328	PRINTS	PR00420	Aromatic-ring hydroxylase (flavoprotein monooxygenase) signature
4	26	PRINTS	PR00420	Aromatic-ring hydroxylase (flavoprotein monooxygenase) signature
151	166	PRINTS	PR00420	Aromatic-ring hydroxylase (flavoprotein monooxygenase) signature
278	293	PRINTS	PR00420	Aromatic-ring hydroxylase (flavoprotein monooxygenase) signature

3D Structure

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

Loading 3D structure...

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Structural evidence

0 + 2

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

Entry	Method	Resolution	Chain	Coverage	Links	Status
AlphaFold AF_A0A0H3GIS2	AlphaFold	—	—	full sequence	—	Viewing
ColabFold VK055_2617	ColabFold	—	—	full sequence	—	Loaded

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
13				0.504
3				0.008
25				0.005
27				0.005

Pockets (P2RANK)

Showing top-ranked P2Rank candidates by probability. Probability is color-coded per P2Rank calibration: high (≥ 0.5), medium (0.2 – 0.49), low (< 0.2).

P2RANK	Score	Probability
1	33.06	0.92
2	2.08	0.039
3	1.09	0.007

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
2				0.719
14				0.049
3				0.003
12				0.003

Pockets (P2RANK)

Showing top-ranked P2Rank candidates by probability. Probability is color-coded per P2Rank calibration: high (≥ 0.5), medium (0.2 – 0.49), low (< 0.2).

P2RANK	Score	Probability
1	37.51	0.94
2	2.26	0.046
3	1.5	0.017
4	1.22	0.01
5	1.08	0.007

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.

62 records

Highest-confidence structural evidence: ligands co-crystallized with this exact protein. If the source PDB is loaded in TPW, use Open crystal to inspect it in the structure viewer.

No PDB structure with a co-crystallized ligand found for this exact protein.

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.

Ligand	Source crystal	UniProt (homolog)	MW · LogP · TPSA	Lipinski	PAINS	SMILES
APR	2PHH	P00438	559.3 Da LogP -3.28 TPSA 291.5	3 viol.	✓ Clean	`c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)…`
BHA	1PBC	P00438	153.1 Da LogP 0.67 TPSA 83.5	✓ Ro5	✓ Clean	`c1cc(c(cc1N)O)C(=O)O`
DHB	6JU1	P20586	154.1 Da LogP 0.80 TPSA 77.8	✓ Ro5	Alert	`c1cc(c(cc1C(=O)O)O)O`
DOB	1DOD	P20586	154.1 Da LogP 0.80 TPSA 77.8	✓ Ro5	✓ Clean	`c1cc(c(cc1O)O)C(=O)O`
FAS	1PDH	P00438	785.6 Da LogP -2.42 TPSA 362.9	3 viol.	✓ Clean	`Cc1cc2c(cc1C)N(C3=NC(=O)NC(=O)C3=N2)C[C@H]([C@@…`
PAB	1IUS	P20586	137.1 Da LogP 0.97 TPSA 63.3	✓ Ro5	✓ Clean	`c1cc(ccc1C(=O)O)N`
PHB	7ON9	C4TP09	138.1 Da LogP 1.09 TPSA 57.5	✓ Ro5	✓ Clean	`c1cc(ccc1C(=O)O)O`
PSL	1YKJ	P20586	176.1 Da LogP -2.08 TPSA 123.6	✓ Ro5	✓ Clean	`[O-]S(=O)(=O)OS(=O)(=O)[O-]`
RFH	6C7S	Q5YTV5	839.0 Da LogP 3.15 TPSA 248.0	2 viol.	Alert	`Cc1c(c2c(c3c1O[C@](C3=O)(C)O/C=C/[C@@H]([C@@H](…`
RFL	1D7L	P20586	814.6 Da LogP -2.67 TPSA 366.2	3 viol.	✓ Clean	`Cc1cc2c(cc1N(C)C)N(C3=NC(=O)NC(=O)C3=N2)C[C@@H]…`
RFP	6BRD	F2R776	823.0 Da LogP 4.34 TPSA 220.1	3 viol.	Alert	`Cc1c(c2c3c4c1O[C@@](C4=O)(O\C=C\[C@@H]([C@H]([C…`

Experimental bioactivity from ChEMBL measured directly on this protein. Score = pchembl (−log Ki/IC₅₀; higher = more potent).

No ChEMBL bioactivity data found for this exact protein.

Bioactivity inferred from similar proteins in ChEMBL. Score = pchembl (−log Ki/IC₅₀; higher = more potent).

Ligand	UniProt (homolog)	pchembl	MW · LogP · TPSA	Lipinski	PAINS	SMILES
CHEMBL130259	P00438	7.23	244.2 Da LogP 2.67 TPSA 66.8	✓ Ro5	✓ Clean	`O=C(O)c1ccc(O)cc1OCc1ccccc1`

Proposed virtual-screening candidates from ZINC. Score = Tanimoto similarity to a known binder (0–1; higher = more similar).

Ligand	Tanimoto	MW · LogP · TPSA	Lipinski	PAINS	SMILES
ZINC1245666585	0.850	289.3 Da LogP 4.30 TPSA 63.3	✓ Ro5	✓ Clean	`Nc1ccc(-c2ccc(-c3ccc(C(=O)O)cc3)cc2)cc1`
ZINC1746121	0.850	213.2 Da LogP 2.63 TPSA 63.3	✓ Ro5	✓ Clean	`Nc1ccc(-c2ccc(C(=O)O)cc2)cc1`
ZINC22018837	0.850	241.2 Da LogP 2.20 TPSA 80.4	✓ Ro5	✓ Clean	`Nc1ccc(C(=O)c2ccc(C(=O)O)cc2)cc1`
ZINC389804	0.842	214.2 Da LogP 2.76 TPSA 57.5	✓ Ro5	✓ Clean	`O=C(O)c1ccc(-c2ccc(O)cc2)cc1`
ZINC100412109	0.739	241.3 Da LogP 3.38 TPSA 88.0	✓ Ro5	Alert	`Nc1ccc(/N=N\c2ccc(C(=O)O)cc2)cc1`
ZINC113407075	0.739	237.3 Da LogP 2.37 TPSA 63.3	✓ Ro5	✓ Clean	`Nc1ccc(C#Cc2ccc(C(=O)O)cc2)cc1`
ZINC127654	0.739	229.2 Da LogP 2.76 TPSA 72.5	✓ Ro5	Alert	`Nc1ccc(Oc2ccc(C(=O)O)cc2)cc1`
ZINC1628139	0.739	239.3 Da LogP 3.14 TPSA 63.3	✓ Ro5	✓ Clean	`Nc1ccc(/C=C/c2ccc(C(=O)O)cc2)cc1`
ZINC17285708	0.739	239.3 Da LogP 3.14 TPSA 63.3	✓ Ro5	✓ Clean	`Nc1ccc(/C=C\c2ccc(C(=O)O)cc2)cc1`
ZINC17322332	0.739	241.3 Da LogP 3.38 TPSA 88.0	✓ Ro5	Alert	`Nc1ccc(N=Nc2ccc(C(=O)O)cc2)cc1`
ZINC1750451	0.739	227.3 Da LogP 2.56 TPSA 63.3	✓ Ro5	Alert	`Nc1ccc(Cc2ccc(C(=O)O)cc2)cc1`
ZINC4707411	0.739	241.3 Da LogP 3.38 TPSA 88.0	✓ Ro5	Alert	`Nc1ccc(/N=N/c2ccc(C(=O)O)cc2)cc1`
ZINC148781474	0.727	274.2 Da LogP 2.16 TPSA 115.1	✓ Ro5	✓ Clean	`O=C(O)c1ccc(-c2ccc(C(=O)O)cc2O)c(O)c1`
ZINC33246180	0.727	242.2 Da LogP 3.51 TPSA 82.2	✓ Ro5	Alert	`O=C(O)c1ccc(N=Nc2ccc(O)cc2)cc1`
ZINC3896282	0.727	242.2 Da LogP 3.51 TPSA 82.2	✓ Ro5	Alert	`O=C(O)c1ccc(/N=N/c2ccc(O)cc2)cc1`
ZINC392302	0.727	230.2 Da LogP 2.88 TPSA 66.8	✓ Ro5	✓ Clean	`O=C(O)c1ccc(Oc2ccc(O)cc2)cc1`
ZINC13084338	0.722	242.3 Da LogP 3.27 TPSA 46.5	✓ Ro5	✓ Clean	`Cc1ccc(C(=O)O)c(OCc2ccccc2)c1`
ZINC91297263	0.722	246.2 Da LogP 3.10 TPSA 46.5	✓ Ro5	✓ Clean	`O=C(O)c1ccc(F)cc1OCc1ccccc1`
ZINC1675321	0.714	274.2 Da LogP 1.57 TPSA 115.1	✓ Ro5	Alert	`O=C(C(=O)c1ccc(O)c(O)c1)c1ccc(O)c(O)c1`
ZINC2169206	0.697	228.2 Da LogP 2.96 TPSA 46.5	✓ Ro5	✓ Clean	`O=C(O)c1ccccc1OCc1ccccc1`
ZINC1587804	0.696	274.2 Da LogP 1.57 TPSA 115.1	✓ Ro5	Alert	`O=C(C(=O)c1ccc(O)cc1O)c1ccc(O)cc1O`
ZINC289893	0.696	278.3 Da LogP 1.92 TPSA 91.7	✓ Ro5	✓ Clean	`O=C(O)c1ccc(S(=O)(=O)c2ccc(O)cc2)cc1`
ZINC39103	0.696	246.2 Da LogP 1.74 TPSA 98.0	✓ Ro5	✓ Clean	`O=C(c1ccc(O)cc1O)c1ccc(O)cc1O`
ZINC1710961	0.684	240.3 Da LogP 1.92 TPSA 86.2	✓ Ro5	Alert	`Nc1ccc(C(=O)C(=O)c2ccc(N)cc2)cc1`
ZINC113749473	0.680	261.3 Da LogP 2.37 TPSA 63.3	✓ Ro5	✓ Clean	`Nc1ccc(C#CC#Cc2ccc(C(=O)O)cc2)cc1`
ZINC439984	0.679	258.2 Da LogP 2.03 TPSA 94.8	✓ Ro5	✓ Clean	`O=C(O)c1ccccc1C(=O)c1ccc(O)cc1O`
ZINC114185151	0.667	298.2 Da LogP 2.15 TPSA 108.7	✓ Ro5	Alert	`O=C(O)c1ccc(C(=O)C(=O)c2ccc(C(=O)O)cc2)cc1`
ZINC146669761	0.667	274.2 Da LogP 2.16 TPSA 115.1	✓ Ro5	✓ Clean	`O=C(O)c1ccc(-c2ccc(C(=O)O)c(O)c2)cc1O`
ZINC2049383980	0.667	286.3 Da LogP 3.75 TPSA 55.8	✓ Ro5	✓ Clean	`CC(C)Oc1ccc(C(=O)O)c(OCc2ccccc2)c1`
ZINC2924369	0.667	242.2 Da LogP 2.16 TPSA 74.6	✓ Ro5	Alert	`O=C(C(=O)c1ccc(O)cc1)c1ccc(O)cc1`
ZINC90712706	0.667	306.4 Da LogP 4.55 TPSA 38.7	✓ Ro5	✓ Clean	`Oc1ccc(OCc2ccccc2)c(OCc2ccccc2)c1`
ZINC95830239	0.667	296.2 Da LogP 3.98 TPSA 46.5	✓ Ro5	✓ Clean	`O=C(O)c1ccc(C(F)(F)F)cc1OCc1ccccc1`
ZINC225984	0.654	256.3 Da LogP 2.22 TPSA 92.4	✓ Ro5	✓ Clean	`Nc1ccc(C(=O)Nc2ccc(C(=O)O)cc2)cc1`
ZINC32303064	0.654	256.3 Da LogP 2.22 TPSA 92.4	✓ Ro5	Alert	`Nc1ccc(NC(=O)c2ccc(C(=O)O)cc2)cc1`
ZINC155329	0.650	212.3 Da LogP 2.08 TPSA 69.1	✓ Ro5	✓ Clean	`Nc1ccc(C(=O)c2ccc(N)cc2)cc1`
ZINC1587673	0.650	273.2 Da LogP 2.87 TPSA 89.7	✓ Ro5	✓ Clean	`O=C(O)c1ccc([N+](=O)[O-])cc1OCc1ccccc1`
ZINC35414218	0.650	286.3 Da LogP 3.75 TPSA 55.8	✓ Ro5	✓ Clean	`CCCOc1ccc(C(=O)O)c(OCc2ccccc2)c1`
ZINC310032990	0.649	264.2 Da LogP 3.24 TPSA 46.5	✓ Ro5	✓ Clean	`O=C(O)c1cc(F)c(F)cc1OCc1ccccc1`
ZINC396144916	0.649	256.3 Da LogP 3.58 TPSA 46.5	✓ Ro5	✓ Clean	`Cc1cc(OCc2ccccc2)c(C(=O)O)cc1C`
ZINC12471554	0.640	217.0 Da LogP 1.85 TPSA 57.5	✓ Ro5	✓ Clean	`O=C(O)c1ccc(Br)c(O)c1`
ZINC161925	0.640	264.0 Da LogP 1.69 TPSA 57.5	✓ Ro5	✓ Clean	`O=C(O)c1ccc(I)c(O)c1`
ZINC2048532660	0.640	350.3 Da LogP 3.83 TPSA 115.1	✓ Ro5	✓ Clean	`O=C(O)c1ccc(-c2ccc(-c3ccc(C(=O)O)c(O)c3)cc2)cc1O`
ZINC2566180	0.640	217.0 Da LogP 1.85 TPSA 57.5	✓ Ro5	✓ Clean	`O=C(O)c1ccc(O)c(Br)c1`
ZINC3156317	0.640	258.2 Da LogP 2.31 TPSA 83.8	✓ Ro5	✓ Clean	`O=C(O)c1ccc(OC(=O)c2ccc(O)cc2)cc1`
ZINC330968	0.640	264.0 Da LogP 1.69 TPSA 57.5	✓ Ro5	✓ Clean	`O=C(O)c1ccc(O)c(I)c1`
ZINC4903179	0.640	257.2 Da LogP 2.34 TPSA 86.6	✓ Ro5	✓ Clean	`O=C(O)c1ccc(NC(=O)c2ccc(O)cc2)cc1`
ZINC6535079	0.640	204.2 Da LogP 1.95 TPSA 77.8	✓ Ro5	Alert	`O=C(O)c1ccc2cc(O)c(O)cc2c1`
ZINC72107312	0.639	244.2 Da LogP 2.67 TPSA 66.8	✓ Ro5	✓ Clean	`O=C(O)c1cccc(OCc2ccccc2)c1O`
ZINC2026240	0.636	225.2 Da LogP 2.33 TPSA 60.2	✓ Ro5	Alert	`Nc1ccc(C(=O)C(=O)c2ccccc2)cc1`
ZINC239025565	0.634	695.8 Da LogP 3.63 TPSA 195.0	2 viol.	Alert	`CO[C@@H]1/C=C/O[C@@]2(C)Oc3c(C)c(O)c4c(c3C2=O)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.