Protein profile

KP13_04441

Protocatechuate 3,4-dioxygenase alpha chain

Genome: KpKP13

Gene: AHE44314.1 Structure source: AlphaFold + ColabFold UniProt A0A0H3GP30

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Amino acids 206

Annotations 7

Features 13

PDB binders 18

Druggability 0.538

Overview

Basic information about this protein and its source genome.

Accession: KP13_04441
Assembly: Klebsiella pneumoniae subsp. pneumoniae Kp13, complete sequence
Gene: AHE44314.1
Status: annotated
Amino acids: 206
Structure source: AlphaFold + ColabFold

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. GO:0018578 Catalysis of the reaction: 3,4-dihydroxybenzoate + O2 = 3-carboxy-cis,cis-muconate. GO:0019439 OBSOLETE. The chemical reactions and pathways resulting in the breakdown of aromatic compounds, any substance containing an aromatic carbon ring. 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:0005506 Binding to an iron (Fe) ion. 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.

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: 96.77

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 0.538

Structure A0A0H3GP30

Pocket Pocket 1

P2Rank 0.094

Structure A0A0H3GP30

Pocket Pocket 1

ColabFold model

FPocket 0.527 · Pocket 8

P2Rank 0.091 · Pocket 1

Core conservation Conserved core gene

Roary core

CoreCruncher core

Gut microbiome 37 / 4744 genomes with a hit

Normalized 0.008

Sequence

Primary amino-acid sequence viewer.

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

7 GO

Gene Ontology (GO)

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.
GO:0018578 Catalysis of the reaction: 3,4-dihydroxybenzoate + O2 = 3-carboxy-cis,cis-muconate.
GO:0019439 OBSOLETE. The chemical reactions and pathways resulting in the breakdown of aromatic compounds, any substance containing an aromatic carbon ring.
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:0005506 Binding to an iron (Fe) ion.
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.
GO:0008199 Binding to a ferric iron ion, Fe(III).

Sequence Features

Domain/signature hits from InterPro and related databases.

13 records

Show feature table

Start	End	DB	Term	Name
1	206	Gene3D	G3DSA:2.60.130.10	Aromatic compound dioxygenase
1	206	InterPro	IPR015889	Intradiol ring-cleavage dioxygenase, core
5	205	PANTHER	PTHR33711	DIOXYGENASE, PUTATIVE (AFU_ORTHOLOGUE AFUA_2G02910)-RELATED
5	205	CDD	cd03463	3,4-PCD_alpha
5	205	InterPro	IPR012786	Protocatechuate 3,4-dioxygenase, alpha subunit
42	196	Pfam	PF00775	Dioxygenase
42	196	InterPro	IPR000627	Intradiol ring-cleavage dioxygenase, C-terminal
8	206	NCBIfam	TIGR02423	protocatechuate 3,4-dioxygenase subunit alpha
8	206	InterPro	IPR012786	Protocatechuate 3,4-dioxygenase, alpha subunit
3	206	SUPERFAMILY	SSF49482	Aromatic compound dioxygenase
3	206	InterPro	IPR015889	Intradiol ring-cleavage dioxygenase, core
51	79	ProSitePatterns	PS00083	Intradiol ring-cleavage dioxygenases signature.
51	79	InterPro	IPR000627	Intradiol ring-cleavage dioxygenase, C-terminal

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_A0A0H3GP30	AlphaFold	—	—	full sequence	—	Viewing
ColabFold KP13_04441	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				0.538
11				0.499
15				0.15
7				0.001

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	3.35	0.094
2	3.22	0.088
3	1.12	0.007
4	0.95	0.004

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
8				0.527
2				0.241
1				0.066
4				0.001

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	3.29	0.091
2	3.09	0.083
3	1.55	0.019

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.

68 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
3HB	3PCB	P00437	138.1 Da LogP 1.09 TPSA 57.5	✓ Ro5	✓ Clean	`c1cc(cc(c1)O)C(=O)O`
3HP	3PCE	P00436	152.1 Da LogP 1.02 TPSA 57.5	✓ Ro5	✓ Clean	`c1cc(cc(c1)O)CC(=O)O`
3N8	4WHQ	P00437	128.1 Da LogP 1.24 TPSA 40.5	✓ Ro5	Alert	`c1cc(c(cc1F)O)O`
3N9	4WHQ	P00437	160.1 Da LogP 0.16 TPSA 66.8	✓ Ro5	✓ Clean	`C1=CC(=O)[C@@](C=C1F)(O)OO`
3NJ	4WHR	P00437	142.1 Da LogP 0.14 TPSA 47.3	✓ Ro5	✓ Clean	`C1=CC(=O)OC(=O)C=C1F`
4HP	3PCG	P00437	152.1 Da LogP 1.02 TPSA 57.5	✓ Ro5	✓ Clean	`c1cc(ccc1CC(=O)O)O`
4NC	3LXV	P00437	155.1 Da LogP 1.01 TPSA 83.6	✓ Ro5	Alert	`c1cc(c(cc1[N+](=O)[O-])O)O`
CAQ	3MI5	P00437	110.1 Da LogP 1.10 TPSA 40.5	✓ Ro5	Alert	`c1ccc(c(c1)O)O`
CHB	3PCH	P00437	172.6 Da LogP 1.74 TPSA 57.5	✓ Ro5	✓ Clean	`c1cc(c(cc1C(=O)O)Cl)O`
DHB	1YKL	P00437	154.1 Da LogP 0.80 TPSA 77.8	✓ Ro5	Alert	`c1cc(c(cc1C(=O)O)O)O`
DHY	3MFL	P00437	168.1 Da LogP 0.72 TPSA 77.8	✓ Ro5	Alert	`c1cc(c(cc1CC(=O)O)O)O`
FHB	3PCF	P00437	156.1 Da LogP 1.23 TPSA 57.5	✓ Ro5	✓ Clean	`c1cc(c(cc1C(=O)O)F)O`
IHB	3PCI	P00437	264.0 Da LogP 1.70 TPSA 57.5	✓ Ro5	✓ Clean	`c1cc(c(cc1C(=O)O)I)O`
INO	3PCJ	P00437	155.1 Da LogP -0.28 TPSA 84.5	✓ Ro5	✓ Clean	`c1c[n+](c(cc1C(=O)O)O)[O-]`
MUC	4WHS	P00437	142.1 Da LogP -0.06 TPSA 63.6	✓ Ro5	✓ Clean	`C1=CC(=O)O[C@H]1CC(=O)O`
NNO	3PCK	P00437	155.1 Da LogP -0.28 TPSA 84.5	✓ Ro5	✓ Clean	`c1cc([n+](cc1C(=O)O)[O-])O`
PHB	3PCC	P00437	138.1 Da LogP 1.09 TPSA 57.5	✓ Ro5	✓ Clean	`c1cc(ccc1C(=O)O)O`
PTY	5TD3	A4JR51	734.1 Da LogP 11.67 TPSA 134.4	2 viol.	✓ Clean	`CCCCCCCCCCCCCCCCCCCC(=O)O[C@H](COC(=O)CCCCCCCCC…`

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
ZINC102190506	1.000	467.5 Da LogP 4.25 TPSA 134.4	✓ Ro5	✓ Clean	`CCCCCCCC(=O)OC[C@H](CO[P@@](=O)(O)OCCN)OC(=O)CC…`
ZINC102190512	1.000	467.5 Da LogP 4.25 TPSA 134.4	✓ Ro5	✓ Clean	`CCCCCCCC(=O)OC[C@@H](CO[P@@](=O)(O)OCCN)OC(=O)C…`
ZINC27416437	0.976	411.4 Da LogP 2.69 TPSA 134.4	✓ Ro5	✓ Clean	`CCCCCC(=O)OC[C@H](CO[P@](=O)(O)OCCN)OC(=O)CCCCC`
ZINC33902364	0.976	411.4 Da LogP 2.69 TPSA 134.4	✓ Ro5	✓ Clean	`CCCCCC(=O)OC[C@@H](CO[P@@](=O)(O)OCCN)OC(=O)CCC…`
ZINC389804	0.842	214.2 Da LogP 2.76 TPSA 57.5	✓ Ro5	✓ Clean	`O=C(O)c1ccc(-c2ccc(O)cc2)cc1`
ZINC32002933	0.786	228.2 Da LogP 2.69 TPSA 57.5	✓ Ro5	✓ Clean	`O=C(O)Cc1cccc(-c2cccc(O)c2)c1`
ZINC13544781	0.771	482.6 Da LogP 4.22 TPSA 108.4	✓ Ro5	✓ Clean	`CCCCCCC(=O)OC[C@@H](CO[P@](=O)(O)OCC[N+](C)(C)C…`
ZINC13544783	0.771	482.6 Da LogP 4.22 TPSA 108.4	✓ Ro5	✓ Clean	`CCCCCCC(=O)OC[C@H](CO[P@](=O)(O)OCC[N+](C)(C)C)…`
ZINC13543439	0.750	454.5 Da LogP 3.44 TPSA 108.4	✓ Ro5	✓ Clean	`CCCCCC(=O)OC[C@@H](CO[P@](=O)(O)OCC[N+](C)(C)C)…`
ZINC13543441	0.750	454.5 Da LogP 3.44 TPSA 108.4	✓ Ro5	✓ Clean	`CCCCCC(=O)OC[C@H](CO[P@](=O)(O)OCC[N+](C)(C)C)O…`
ZINC102190945	0.739	411.5 Da LogP 3.29 TPSA 128.3	✓ Ro5	✓ Clean	`CCCCCCCCCCCCC(=O)OC[C@@H](O)CO[P@@](=O)(O)OCCN`
ZINC32840692	0.739	425.5 Da LogP 3.68 TPSA 128.3	✓ Ro5	✓ Clean	`CCCCCCCCCCCCCC(=O)OC[C@@H](O)CO[P@](=O)(O)OCCN`
ZINC32840693	0.739	425.5 Da LogP 3.68 TPSA 128.3	✓ Ro5	✓ Clean	`CCCCCCCCCCCCCC(=O)OC[C@H](O)CO[P@](=O)(O)OCCN`
ZINC32840704	0.739	453.6 Da LogP 4.46 TPSA 128.3	✓ Ro5	✓ Clean	`CCCCCCCCCCCCCCCC(=O)OC[C@@H](O)CO[P@](=O)(O)OCCN`
ZINC32840705	0.739	453.6 Da LogP 4.46 TPSA 128.3	✓ Ro5	✓ Clean	`CCCCCCCCCCCCCCCC(=O)OC[C@H](O)CO[P@](=O)(O)OCCN`
ZINC95635984	0.739	397.4 Da LogP 2.90 TPSA 128.3	✓ Ro5	✓ Clean	`CCCCCCCCCCCC(=O)OC[C@@H](O)CO[P@@](=O)(O)OCCN`
ZINC102191119	0.729	498.6 Da LogP 3.65 TPSA 148.8	✓ Ro5	✓ Clean	`CCCCCCCC(=O)OC[C@H](CO[P@@](=O)(O)OC[C@@H](O)CO…`
ZINC58649551	0.729	498.6 Da LogP 3.65 TPSA 148.8	✓ Ro5	✓ Clean	`CCCCCCCC(=O)OC[C@H](CO[P@@](=O)(O)OC[C@H](O)CO)…`
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`
ZINC36178999	0.727	424.5 Da LogP 4.27 TPSA 119.4	✓ Ro5	✓ Clean	`CCCCCCCC(=O)OC[C@@H](COP(=O)(O)O)OC(=O)CCCCCCC`
ZINC36179002	0.727	424.5 Da LogP 4.27 TPSA 119.4	✓ Ro5	✓ Clean	`CCCCCCCC(=O)OC[C@H](COP(=O)(O)O)OC(=O)CCCCCCC`
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`
ZINC39410336	0.727	242.2 Da LogP 2.16 TPSA 74.6	✓ Ro5	Alert	`O=C(C(=O)c1cccc(O)c1)c1cccc(O)c1`
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)…`
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`
ZINC13543394	0.708	455.4 Da LogP 2.15 TPSA 171.7	✓ Ro5	✓ Clean	`CCCCCC(=O)OC[C@H](CO[P@@](=O)(O)OC[C@H](N)C(=O)…`
ZINC5820131	0.705	368.4 Da LogP 2.71 TPSA 119.4	✓ Ro5	✓ Clean	`CCCCCC(=O)OC[C@@H](COP(=O)(O)O)OC(=O)CCCCC`
ZINC5820134	0.705	368.4 Da LogP 2.71 TPSA 119.4	✓ Ro5	✓ Clean	`CCCCCC(=O)OC[C@H](COP(=O)(O)O)OC(=O)CCCCC`
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`
ZINC33822387	0.694	426.5 Da LogP 2.66 TPSA 108.4	✓ Ro5	✓ Clean	`CCCCC(=O)OC[C@H](CO[P@@](=O)(O)OCC[N+](C)(C)C)O…`
ZINC33822389	0.694	426.5 Da LogP 2.66 TPSA 108.4	✓ Ro5	✓ Clean	`CCCCC(=O)OC[C@@H](CO[P@@](=O)(O)OCC[N+](C)(C)C)…`
ZINC1682664	0.682	270.3 Da LogP 2.61 TPSA 74.6	✓ Ro5	✓ Clean	`O=C(O)Cc1ccc(-c2ccc(CC(=O)O)cc2)cc1`
ZINC391495	0.682	298.3 Da LogP 2.73 TPSA 74.6	✓ Ro5	✓ Clean	`O=C(O)Cc1ccc(CCc2ccc(CC(=O)O)cc2)cc1`
ZINC2566063	0.679	231.0 Da LogP 1.78 TPSA 57.5	✓ Ro5	✓ Clean	`O=C(O)Cc1ccc(O)c(Br)c1`
ZINC83072638	0.679	231.0 Da LogP 1.78 TPSA 57.5	✓ Ro5	✓ Clean	`O=C(O)Cc1ccc(Br)c(O)c1`
ZINC96334879	0.679	278.0 Da LogP 1.62 TPSA 57.5	✓ Ro5	✓ Clean	`O=C(O)Cc1ccc(O)c(I)c1`
ZINC42417744	0.677	209.2 Da LogP 0.14 TPSA 86.6	✓ Ro5	✓ Clean	`O=C(O)CNC(=O)Cc1cccc(O)c1`
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`
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`
ZINC2924369	0.667	242.2 Da LogP 2.16 TPSA 74.6	✓ Ro5	Alert	`O=C(C(=O)c1ccc(O)cc1)c1ccc(O)cc1`
ZINC352067517	0.667	205.2 Da LogP 2.16 TPSA 83.6	✓ Ro5	Alert	`O=[N+]([O-])c1ccc2cc(O)c(O)cc2c1`
ZINC575442763	0.667	314.3 Da LogP 2.66 TPSA 83.8	✓ Ro5	✓ Clean	`O=C(O)Cc1ccc(COCc2ccc(CC(=O)O)cc2)cc1`
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`
ZINC1501016364	0.654	465.6 Da LogP 4.63 TPSA 128.3	✓ Ro5	✓ Clean	`CCCCCC/C=C\CCCCCCCCC(=O)OC[C@@H](O)CO[P@](=O)(O…`
ZINC32153033	0.650	222.2 Da LogP 3.04 TPSA 40.5	✓ Ro5	✓ Clean	`Oc1ccc(F)cc1-c1cc(F)ccc1O`
ZINC139174928	0.645	228.2 Da LogP 2.69 TPSA 57.5	✓ Ro5	✓ Clean	`O=C(O)Cc1ccc(-c2cccc(O)c2)cc1`

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.