Protein profile

KP13_07626

Protocatechuate 4,5-dioxygenase beta chain

Genome: KpKP13

Gene: ANJ86560.1 Structure source: AlphaFold + ColabFold UniProt A0A0H3H4Q3

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Amino acids 420

Annotations 4

Features 14

PDB binders 2

Druggability 0.488

Overview

Basic information about this protein and its source genome.

Accession: KP13_07626
Assembly: Klebsiella pneumoniae subsp. pneumoniae Kp13, complete sequence
Gene: ANJ86560.1
Status: annotated
Amino acids: 420
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: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. GO:0016702 Catalysis of an oxidation-reduction (redox) reaction in which hydrogen or electrons are transferred from one donor, and two oxygen atoms is incorporated into a donor.

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: Unknown
ColabFold pLDDT: 96.81

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 0.488

Structure A0A0H3H4Q3

Pocket Pocket 4

P2Rank 0.709

Structure A0A0H3H4Q3

Pocket Pocket 1

ColabFold model

FPocket 0.383 · Pocket 1

P2Rank 0.662 · Pocket 1

Core conservation Accessory gene

Roary accessory

CoreCruncher accessory

Gut microbiome 14 / 4744 genomes with a hit

Normalized 0.003

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: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.
GO:0016702 Catalysis of an oxidation-reduction (redox) reaction in which hydrogen or electrons are transferred from one donor, and two oxygen atoms is incorporated into a donor.

Sequence Features

Domain/signature hits from InterPro and related databases.

14 records

Show feature table

Start	End	DB	Term	Name
308	420	Gene3D	G3DSA:1.10.700.10	Dioxygenase LigAB, LigA subunit
308	420	InterPro	IPR036622	Dioxygenase LigAB, LigA subunit superfamily
323	409	Pfam	PF07746	Aromatic-ring-opening dioxygenase LigAB, LigA subunit
323	409	InterPro	IPR011986	Extradiol ring-cleavage dioxygenase LigAB, LigA subunit
294	419	SUPERFAMILY	SSF48076	LigA subunit of an aromatic-ring-opening dioxygenase LigAB
294	419	InterPro	IPR036622	Dioxygenase LigAB, LigA subunit superfamily
8	270	Pfam	PF02900	Catalytic LigB subunit of aromatic ring-opening dioxygenase
8	270	InterPro	IPR004183	Extradiol ring-cleavage dioxygenase, class III enzyme, subunit B
1	279	CDD	cd07950	Gallate_Doxase_N
1	279	InterPro	IPR034939	Gallate dioxygenase, N-terminal
2	296	SUPERFAMILY	SSF53213	LigB-like
316	409	CDD	cd07923	Gallate_dioxygenase_C
316	409	InterPro	IPR034940	Gallate dioxygenase, C-terminal
3	307	Gene3D	G3DSA:3.40.830.10	-

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_A0A0H3H4Q3	AlphaFold	—	—	full sequence	—	Viewing
ColabFold KP13_07626	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
1				0.413
23				0.006
28				0.003
3				0.002

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	16.76	0.709
2	2.34	0.05
3	1.84	0.03

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				0.383

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				10.19	0.548
2				1.33	0.015

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.

52 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
DHB	1B4U	P22635	154.1 Da LogP 0.80 TPSA 77.8	✓ Ro5	Alert	`c1cc(c(cc1C(=O)O)O)O`
GDE	3WR9	Q5NTE5	170.1 Da LogP 0.50 TPSA 98.0	✓ Ro5	Alert	`c1c(cc(c(c1O)O)O)C(=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
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`
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`
ZINC400170	0.696	233.0 Da LogP 1.56 TPSA 77.8	✓ Ro5	Alert	`O=C(O)c1cc(O)c(O)c(Br)c1`
ZINC2048532784	0.667	248.2 Da LogP 1.65 TPSA 115.1	✓ Ro5	✓ Clean	`O=C(O)c1cc(O)c2cc(C(=O)O)cc(O)c2c1`
ZINC225723980	0.667	212.2 Da LogP 0.42 TPSA 115.1	✓ Ro5	Alert	`O=C(O)Cc1cc(C(=O)O)cc(O)c1O`
ZINC3869510	0.654	322.2 Da LogP 1.13 TPSA 164.8	1 viol.	Alert	`O=C(O)c1cc(O)c(O)c(OC(=O)c2cc(O)c(O)c(O)c2)c1`
ZINC5783979	0.654	322.2 Da LogP 1.13 TPSA 164.8	1 viol.	Alert	`O=C(O)c1cc(O)c(OC(=O)c2cc(O)c(O)c(O)c2)c(O)c1`
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`
ZINC2566180	0.640	217.0 Da LogP 1.85 TPSA 57.5	✓ Ro5	✓ Clean	`O=C(O)c1ccc(O)c(Br)c1`
ZINC330968	0.640	264.0 Da LogP 1.69 TPSA 57.5	✓ Ro5	✓ Clean	`O=C(O)c1ccc(O)c(I)c1`
ZINC6535079	0.640	204.2 Da LogP 1.95 TPSA 77.8	✓ Ro5	Alert	`O=C(O)c1ccc2cc(O)c(O)cc2c1`
ZINC5046520	0.636	280.0 Da LogP 1.40 TPSA 77.8	✓ Ro5	✓ Clean	`O=C(O)c1cc(O)c(I)c(O)c1`
ZINC56611	0.636	233.0 Da LogP 1.56 TPSA 77.8	✓ Ro5	✓ Clean	`O=C(O)c1cc(O)c(Br)c(O)c1`
ZINC262158	0.615	214.2 Da LogP 2.33 TPSA 57.5	✓ Ro5	Alert	`O=C(c1ccccc1)c1ccc(O)c(O)c1`
ZINC65350651	0.615	258.2 Da LogP 2.46 TPSA 94.8	✓ Ro5	✓ Clean	`O=C(O)c1ccc(-c2ccc(C(=O)O)cc2O)cc1`
ZINC391981	0.611	210.1 Da LogP 0.78 TPSA 111.9	✓ Ro5	✓ Clean	`O=C(O)c1cc(C(=O)O)cc(C(=O)O)c1`
ZINC3843448	0.609	320.3 Da LogP 1.50 TPSA 155.5	1 viol.	✓ Clean	`O=C(O)c1cc(O)c(Cc2c(O)cc(C(=O)O)cc2O)c(O)c1`
ZINC2572877	0.593	206.1 Da LogP 2.11 TPSA 57.5	✓ Ro5	✓ Clean	`O=C(O)c1ccc(O)c(C(F)(F)F)c1`
ZINC44559904	0.593	214.2 Da LogP 2.76 TPSA 57.5	✓ Ro5	✓ Clean	`O=C(O)c1ccc(-c2ccccc2)c(O)c1`
ZINC71260675	0.593	206.1 Da LogP 2.11 TPSA 57.5	✓ Ro5	✓ Clean	`O=C(O)c1ccc(C(F)(F)F)c(O)c1`
ZINC142873985	0.586	222.1 Da LogP 1.99 TPSA 66.8	✓ Ro5	✓ Clean	`O=C(O)c1ccc(O)c(OC(F)(F)F)c1`
ZINC21950888	0.571	214.2 Da LogP 2.76 TPSA 57.5	✓ Ro5	✓ Clean	`O=C(O)c1ccc(O)c(-c2ccccc2)c1`
ZINC21967846	0.571	217.2 Da LogP -0.26 TPSA 117.7	✓ Ro5	✓ Clean	`NS(=O)(=O)c1cc(C(=O)O)ccc1O`
ZINC65350194	0.571	248.2 Da LogP 2.60 TPSA 77.8	✓ Ro5	✓ Clean	`O=C(O)c1ccc(-c2ccc(F)cc2O)c(O)c1`
ZINC156288	0.565	216.2 Da LogP 2.24 TPSA 74.6	✓ Ro5	✓ Clean	`O=C(O)c1ccc2cc(C(=O)O)ccc2c1`
ZINC156492	0.565	207.0 Da LogP 2.40 TPSA 57.5	✓ Ro5	✓ Clean	`O=C(O)c1cc(Cl)c(O)c(Cl)c1`
ZINC4099416	0.565	389.9 Da LogP 2.30 TPSA 57.5	✓ Ro5	✓ Clean	`O=C(O)c1cc(I)c(O)c(I)c1`
ZINC56596	0.565	295.9 Da LogP 2.62 TPSA 57.5	✓ Ro5	✓ Clean	`O=C(O)c1cc(Br)c(O)c(Br)c1`
ZINC116231002	0.560	207.0 Da LogP 2.40 TPSA 57.5	✓ Ro5	✓ Clean	`O=C(O)c1cc(O)c(Cl)c(Cl)c1`
ZINC575693807	0.560	295.9 Da LogP 2.62 TPSA 57.5	✓ Ro5	✓ Clean	`O=C(O)c1cc(O)c(Br)c(Br)c1`
ZINC3983883	0.556	262.2 Da LogP 1.45 TPSA 118.2	✓ Ro5	Alert	`O=C(c1ccc(O)c(O)c1)c1c(O)cc(O)cc1O`
ZINC1702059	0.552	264.2 Da LogP 0.72 TPSA 135.3	✓ Ro5	Alert	`O=C(O)c1cc(O)c(=O)c2c(O)c(O)c(O)cc2c1`
ZINC225723197	0.552	211.2 Da LogP 0.86 TPSA 81.0	✓ Ro5	Alert	`CN(C)Cc1cc(C(=O)O)cc(O)c1O`
ZINC2528279	0.542	216.2 Da LogP 2.24 TPSA 74.6	✓ Ro5	✓ Clean	`O=C(O)c1ccc2ccc(C(=O)O)cc2c1`
ZINC2579274	0.542	240.2 Da LogP 2.73 TPSA 74.6	✓ Ro5	✓ Clean	`O=C(O)c1ccc2c(c1)-c1ccc(C(=O)O)cc1-2`
ZINC642881183	0.538	350.3 Da LogP 3.83 TPSA 115.1	✓ Ro5	✓ Clean	`O=C(O)c1ccc(-c2cc(O)c(-c3ccc(C(=O)O)cc3)cc2O)cc1`
ZINC202705328	0.536	334.3 Da LogP 1.52 TPSA 133.5	✓ Ro5	Alert	`O=C(OCCOC(=O)c1ccc(O)c(O)c1)c1ccc(O)c(O)c1`
ZINC22005628	0.536	248.7 Da LogP 2.98 TPSA 57.5	✓ Ro5	Alert	`O=C(c1ccc(Cl)cc1)c1ccc(O)c(O)c1`
ZINC77286769	0.536	228.2 Da LogP 2.64 TPSA 57.5	✓ Ro5	Alert	`Cc1ccc(C(=O)c2ccc(O)c(O)c2)cc1`
ZINC142447986	0.533	211.2 Da LogP -0.09 TPSA 106.9	✓ Ro5	Alert	`O=C(O)CNC(=O)c1ccc(O)c(O)c1`
ZINC5664846	0.533	284.2 Da LogP 1.57 TPSA 111.9	✓ Ro5	Alert	`O=C(O)c1ccc2c(c1)C(=O)c1c(O)ccc(O)c1C2=O`
ZINC685964134	0.533	243.1 Da LogP 2.46 TPSA 57.5	✓ Ro5	✓ Clean	`O=C(O)c1ccc(O)c(/C=C/Br)c1`
ZINC96027101	0.533	223.3 Da LogP 1.62 TPSA 60.8	✓ Ro5	Alert	`CN(C)C(C)(C)C(=O)c1ccc(O)c(O)c1`
ZINC113608046	0.524	358.3 Da LogP 1.71 TPSA 166.3	✓ Ro5	✓ Clean	`O=C(O)c1cc(C(=O)O)cc(C(=O)c2cc(C(=O)O)cc(C(=O)O…`
ZINC34751368	0.524	330.2 Da LogP 2.15 TPSA 149.2	✓ Ro5	✓ Clean	`O=C(O)c1cc(C(=O)O)cc(-c2cc(C(=O)O)cc(C(=O)O)c2)…`
ZINC105301	0.520	210.1 Da LogP 0.78 TPSA 111.9	✓ Ro5	✓ Clean	`O=C(O)c1ccc(C(=O)O)c(C(=O)O)c1`
ZINC157888	0.520	250.3 Da LogP 3.69 TPSA 57.5	✓ Ro5	✓ Clean	`CC(C)(C)c1cc(C(=O)O)cc(C(C)(C)C)c1O`
ZINC2599161	0.520	266.3 Da LogP 3.39 TPSA 74.6	✓ Ro5	✓ Clean	`O=C(O)c1ccc2cc3cc(C(=O)O)ccc3cc2c1`
ZINC216722174	0.519	231.0 Da LogP 2.16 TPSA 57.5	✓ Ro5	✓ Clean	`Cc1cc(C(=O)O)cc(O)c1Br`

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.