Protein profile

KP13_16086

3,4-dihydroxyphenylacetate 2,3-dioxygenase

Genome: KpKP13

Gene: hpcB ANJ86632.1 Structure source: AlphaFold + ColabFold UniProt A0A0H3GHT6

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Amino acids 285

Annotations 4

Features 9

PDB binders 3

Druggability 0.714

Overview

Basic information about this protein and its source genome.

Accession: KP13_16086
Assembly: Klebsiella pneumoniae subsp. pneumoniae Kp13, complete sequence
Gene: hpcB ANJ86632.1
Status: annotated
Amino acids: 285
Structure source: AlphaFold + ColabFold

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. GO:0008198 Binding to a ferrous iron ion, Fe(II). GO:0008687 Catalysis of the reaction: 3,4-dihydroxyphenylacetate + O2 = 5-formyl-2-hydroxyhepta-2,4-dienedioate + H+. GO:0006725 OBSOLETE. The chemical reactions and pathways involving aromatic compounds, any organic compound characterized by one or more planar rings, each of which contains conjugated double bonds and delocalized pi electrons, as carried out by individual cells.

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 (%): 0.0
Localization: Cytoplasmic
ColabFold pLDDT: 97.0

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 0.714

Structure A0A0H3GHT6

Pocket Pocket 9

P2Rank 0.683

Structure A0A0H3GHT6

Pocket Pocket 1

ColabFold model

FPocket 0.069 · Pocket 13

P2Rank 0.672 · Pocket 1

Core conservation Conserved core gene

Roary core

CoreCruncher core

Gut microbiome 55 / 4744 genomes with a hit

Normalized 0.012

Sequence

Primary amino-acid sequence viewer.

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

4 GO

Gene Ontology (GO)

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.
GO:0008198 Binding to a ferrous iron ion, Fe(II).
GO:0008687 Catalysis of the reaction: 3,4-dihydroxyphenylacetate + O2 = 5-formyl-2-hydroxyhepta-2,4-dienedioate + H+.
GO:0006725 OBSOLETE. The chemical reactions and pathways involving aromatic compounds, any organic compound characterized by one or more planar rings, each of which contains conjugated double bonds and delocalized pi electrons, as carried out by individual cells.

Sequence Features

Domain/signature hits from InterPro and related databases.

9 records

Show feature table

Start	End	DB	Term	Name
7	279	Pfam	PF02900	Catalytic LigB subunit of aromatic ring-opening dioxygenase
7	279	InterPro	IPR004183	Extradiol ring-cleavage dioxygenase, class III enzyme, subunit B
3	281	Gene3D	G3DSA:3.40.830.10	-
1	281	NCBIfam	TIGR02298	3,4-dihydroxyphenylacetate 2,3-dioxygenase
1	281	InterPro	IPR011984	3,4-dihydroxyphenylacetate 2,3-dioxygenase
12	279	SUPERFAMILY	SSF53213	LigB-like
3	281	CDD	cd07370	HPCD
3	281	InterPro	IPR011984	3,4-dihydroxyphenylacetate 2,3-dioxygenase
10	276	PANTHER	PTHR30096	UNCHARACTERIZED

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_A0A0H3GHT6	AlphaFold	—	—	full sequence	—	Viewing
ColabFold KP13_16086	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
9				0.714

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	Sticks	Spheres	Surfaces	Score	Probability	Labels	Zoom	Positions
1				11.06	0.593
2				3.34	0.118

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	Sticks	Spheres	Surfaces	Score	Probability	Labels	Zoom	Positions
1				10.69	0.574

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.

53 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
2X7	3VSJ	Q6J1Z6	123.1 Da LogP 0.12 TPSA 54.1	✓ Ro5	✓ Clean	`[H]/N=C/1\C=CC=COC1=O`
2XP	3VSJ	Q6J1Z6	141.1 Da LogP 0.24 TPSA 78.2	✓ Ro5	✓ Clean	`[H]/N=C(/C/C=C\C=O)\C(=O)O`
4NC	3VSI	Q6J1Z6	155.1 Da LogP 1.01 TPSA 83.6	✓ Ro5	Alert	`c1cc(c(cc1[N+](=O)[O-])O)O`

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).

No ChEMBL hits found through similar proteins.

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
ZINC36019045	0.720	276.2 Da LogP 2.58 TPSA 126.7	✓ Ro5	✓ Clean	`O=[N+]([O-])c1ccc(O)c(-c2cc([N+](=O)[O-])ccc2O)…`
ZINC1726237	0.667	265.0 Da LogP 1.90 TPSA 63.4	✓ Ro5	✓ Clean	`O=[N+]([O-])c1ccc(O)c(I)c1`
ZINC1750322	0.667	218.0 Da LogP 2.06 TPSA 63.4	✓ Ro5	✓ Clean	`O=[N+]([O-])c1ccc(O)c(Br)c1`
ZINC352067517	0.667	205.2 Da LogP 2.16 TPSA 83.6	✓ Ro5	Alert	`O=[N+]([O-])c1ccc2cc(O)c(O)cc2c1`
ZINC60007417	0.667	265.0 Da LogP 1.90 TPSA 63.4	✓ Ro5	✓ Clean	`O=[N+]([O-])c1ccc(I)c(O)c1`
ZINC91682324	0.667	218.0 Da LogP 2.06 TPSA 63.4	✓ Ro5	✓ Clean	`O=[N+]([O-])c1ccc(Br)c(O)c1`
ZINC31623633	0.643	290.2 Da LogP 2.51 TPSA 126.7	✓ Ro5	✓ Clean	`O=[N+]([O-])c1ccc(O)c(Cc2cc([N+](=O)[O-])ccc2O)…`
ZINC12359019	0.633	259.2 Da LogP 3.42 TPSA 108.3	✓ Ro5	Alert	`O=[N+]([O-])c1ccc(/N=N/c2ccc(O)c(O)c2)cc1`
ZINC96068546	0.633	259.2 Da LogP 3.42 TPSA 108.3	✓ Ro5	Alert	`O=[N+]([O-])c1ccc(N=Nc2ccc(O)c(O)c2)cc1`
ZINC68675213	0.621	234.2 Da LogP 2.36 TPSA 106.5	✓ Ro5	✓ Clean	`O=[N+]([O-])c1ccc2c(O)cc([N+](=O)[O-])cc2c1`
ZINC1724272	0.600	219.2 Da LogP 0.55 TPSA 117.7	✓ Ro5	✓ Clean	`O=[N+]([O-])c1ccc(O)c(S(=O)(=O)O)c1`
ZINC201968930	0.600	218.2 Da LogP -0.05 TPSA 123.5	✓ Ro5	✓ Clean	`NS(=O)(=O)c1ccc([N+](=O)[O-])cc1O`
ZINC32914724	0.600	207.1 Da LogP 2.32 TPSA 63.4	✓ Ro5	✓ Clean	`O=[N+]([O-])c1ccc(O)c(C(F)(F)F)c1`
ZINC84193183	0.600	218.2 Da LogP -0.05 TPSA 123.5	✓ Ro5	✓ Clean	`NS(=O)(=O)c1cc([N+](=O)[O-])ccc1O`
ZINC91366454	0.600	207.1 Da LogP 2.32 TPSA 63.4	✓ Ro5	✓ Clean	`O=[N+]([O-])c1ccc(C(F)(F)F)c(O)c1`
ZINC15443205	0.581	217.2 Da LogP 0.70 TPSA 97.5	✓ Ro5	✓ Clean	`CS(=O)(=O)c1cc([N+](=O)[O-])ccc1O`
ZINC17158509	0.581	330.3 Da LogP 2.37 TPSA 151.5	✓ Ro5	Alert	`O=[N+]([O-])c1ccc(O)c(/C=N\N=C/c2cc([N+](=O)[O-…`
ZINC5732217	0.581	330.3 Da LogP 2.37 TPSA 151.5	✓ Ro5	Alert	`O=[N+]([O-])c1ccc(O)c(/C=N\N=C\c2cc([N+](=O)[O-…`
ZINC6861885	0.581	330.3 Da LogP 2.37 TPSA 151.5	✓ Ro5	Alert	`O=[N+]([O-])c1ccc(O)c(/C=N/N=C/c2cc([N+](=O)[O-…`
ZINC84191264	0.581	215.2 Da LogP 2.97 TPSA 63.4	✓ Ro5	✓ Clean	`O=[N+]([O-])c1ccc(O)c(-c2ccccc2)c1`
ZINC95495694	0.581	217.2 Da LogP 0.70 TPSA 97.5	✓ Ro5	✓ Clean	`CS(=O)(=O)c1ccc([N+](=O)[O-])cc1O`
ZINC1716715	0.563	234.2 Da LogP 2.36 TPSA 106.5	✓ Ro5	✓ Clean	`O=[N+]([O-])c1ccc2c([N+](=O)[O-])c(O)ccc2c1`
ZINC4615055	0.563	204.2 Da LogP 2.09 TPSA 68.3	✓ Ro5	✓ Clean	`O=[N+]([O-])c1ccc(-n2cccc2)c(O)c1`
ZINC32252508	0.560	218.2 Da LogP 2.66 TPSA 86.3	✓ Ro5	✓ Clean	`O=[N+]([O-])c1ccc2cc([N+](=O)[O-])ccc2c1`
ZINC536953409	0.548	249.7 Da LogP 3.62 TPSA 63.4	✓ Ro5	✓ Clean	`O=[N+]([O-])c1ccc(-c2ccc(O)c(Cl)c2)cc1`
ZINC100004378	0.545	320.2 Da LogP 2.86 TPSA 161.7	✓ Ro5	✓ Clean	`O=[N+]([O-])c1ccc(Nc2ccc([N+](=O)[O-])cc2[N+](=…`
ZINC146403874	0.545	223.1 Da LogP 2.20 TPSA 72.6	✓ Ro5	✓ Clean	`O=[N+]([O-])c1ccc(OC(F)(F)F)c(O)c1`
ZINC2046903	0.545	235.2 Da LogP 0.48 TPSA 127.0	✓ Ro5	✓ Clean	`O=[N+]([O-])c1ccc(O)c(OS(=O)(=O)O)c1`
ZINC28294429	0.545	349.3 Da LogP 1.87 TPSA 150.2	✓ Ro5	Alert	`O=[N+]([O-])c1ccc(O)c(CN(CO)Cc2cc([N+](=O)[O-])…`
ZINC294699	0.545	211.2 Da LogP 1.51 TPSA 63.4	✓ Ro5	Alert	`C[N+](C)(C)Cc1ccc([N+](=O)[O-])cc1O`
ZINC35024584	0.545	214.3 Da LogP 1.68 TPSA 63.4	✓ Ro5	✓ Clean	`C[S+](C)Cc1cc([N+](=O)[O-])ccc1O`
ZINC4014057	0.545	210.2 Da LogP 1.00 TPSA 83.7	✓ Ro5	✓ Clean	`CN(C)C(=O)c1cc([N+](=O)[O-])ccc1O`
ZINC66111171	0.545	206.2 Da LogP 0.88 TPSA 94.1	✓ Ro5	✓ Clean	`O=[N+]([O-])c1ccc(O)c(-n2cnnc2)c1`
ZINC66111174	0.545	206.2 Da LogP 0.88 TPSA 94.1	✓ Ro5	✓ Clean	`O=[N+]([O-])c1ccc(-n2cnnc2)c(O)c1`
ZINC85476722	0.545	223.1 Da LogP 2.20 TPSA 72.6	✓ Ro5	✓ Clean	`O=[N+]([O-])c1ccc(O)c(OC(F)(F)F)c1`
ZINC5568338	0.543	303.2 Da LogP 2.66 TPSA 139.1	✓ Ro5	Alert	`O=[N+]([O-])c1ccc(/N=C/c2cc([N+](=O)[O-])ccc2O)…`
ZINC2168662	0.538	218.2 Da LogP 2.66 TPSA 86.3	✓ Ro5	✓ Clean	`O=[N+]([O-])c1ccc2ccc([N+](=O)[O-])cc2c1`
ZINC100456108	0.529	287.2 Da LogP 2.96 TPSA 118.9	✓ Ro5	Alert	`O=[N+]([O-])c1ccc(/C=N/c2ccc([N+](=O)[O-])cc2O)…`
ZINC103653274	0.529	358.3 Da LogP 2.45 TPSA 151.5	✓ Ro5	✓ Clean	`O=[N+]([O-])c1ccc(O)c(/C=N\CC/N=C\c2cc([N+](=O)…`
ZINC15772486	0.529	406.4 Da LogP 4.42 TPSA 151.5	✓ Ro5	✓ Clean	`O=[N+]([O-])c1ccc(O)c(/C=N\c2ccc(/N=C/c3cc([N+]…`
ZINC1644610	0.529	406.4 Da LogP 4.42 TPSA 151.5	✓ Ro5	Alert	`O=[N+]([O-])c1ccc(O)c(/N=C/c2ccc(/C=N/c3cc([N+]…`
ZINC1670414	0.529	358.3 Da LogP 2.45 TPSA 151.5	✓ Ro5	✓ Clean	`O=[N+]([O-])c1ccc(O)c(/C=N/CC/N=C/c2cc([N+](=O)…`
ZINC16997814	0.529	406.4 Da LogP 4.42 TPSA 151.5	✓ Ro5	Alert	`O=[N+]([O-])c1ccc(O)c(/N=C\c2ccc(/C=N/c3cc([N+]…`
ZINC20268444	0.529	229.2 Da LogP 2.89 TPSA 63.4	✓ Ro5	✓ Clean	`O=[N+]([O-])c1ccc(O)c(Cc2ccccc2)c1`
ZINC307639619	0.529	265.1 Da LogP 1.60 TPSA 81.8	✓ Ro5	✓ Clean	`CC1(C)OB(c2ccc([N+](=O)[O-])cc2O)OC1(C)C`
ZINC3153934	0.529	287.2 Da LogP 2.96 TPSA 118.9	✓ Ro5	Alert	`O=[N+]([O-])c1ccc(/C=N/c2cc([N+](=O)[O-])ccc2O)…`
ZINC35583886	0.529	243.3 Da LogP 2.78 TPSA 63.4	✓ Ro5	✓ Clean	`O=[N+]([O-])c1ccc(O)c(C2SCCS2)c1`
ZINC36020548	0.529	438.4 Da LogP 3.42 TPSA 184.9	✓ Ro5	✓ Clean	`O=C(Nc1cc([N+](=O)[O-])ccc1O)c1ccc(C(=O)Nc2cc([…`
ZINC43190938	0.529	416.3 Da LogP 1.51 TPSA 167.4	✓ Ro5	✓ Clean	`O=C(c1cc([N+](=O)[O-])ccc1O)N1CCN(C(=O)c2cc([N+…`
ZINC43190941	0.529	438.4 Da LogP 3.42 TPSA 184.9	✓ Ro5	✓ Clean	`O=C(Nc1ccc(NC(=O)c2cc([N+](=O)[O-])ccc2O)cc1)c1…`

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.