Protein profile

KP13_04442

Protocatechuate 3,4-dioxygenase beta chain

Genome: KpKP13

Gene: AHE44315.1 Structure source: AlphaFold + ColabFold UniProt A0A0H3GYR7

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Amino acids 246

Annotations 7

Features 15

PDB binders 25

Druggability 0.619

Overview

Basic information about this protein and its source genome.

Accession: KP13_04442
Assembly: Klebsiella pneumoniae subsp. pneumoniae Kp13, complete sequence
Gene: AHE44315.1
Status: annotated
Amino acids: 246
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: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:0019619 The chemical reactions and pathways resulting in the breakdown of 3,4-dihydroxybenzoate. 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: 93.09

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 0.619

Structure A0A0H3GYR7

Pocket Pocket 17

P2Rank 0.356

Structure A0A0H3GYR7

Pocket Pocket 1

ColabFold model

FPocket 0.113 · Pocket 10

P2Rank 0.248 · Pocket 1

Core conservation Conserved core gene

Roary core

CoreCruncher core

Gut microbiome 40 / 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: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:0019619 The chemical reactions and pathways resulting in the breakdown of 3,4-dihydroxybenzoate.
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.

15 records

Show feature table

Start	End	DB	Term	Name
4	242	Gene3D	G3DSA:2.60.130.10	Aromatic compound dioxygenase
4	242	InterPro	IPR015889	Intradiol ring-cleavage dioxygenase, core
18	239	NCBIfam	TIGR02422	protocatechuate 3,4-dioxygenase subunit beta
18	239	InterPro	IPR012785	Protocatechuate 3,4-dioxygenase, beta subunit
82	110	ProSitePatterns	PS00083	Intradiol ring-cleavage dioxygenases signature.
82	110	InterPro	IPR000627	Intradiol ring-cleavage dioxygenase, C-terminal
48	230	Pfam	PF00775	Dioxygenase
48	230	InterPro	IPR000627	Intradiol ring-cleavage dioxygenase, C-terminal
13	234	CDD	cd03464	3,4-PCD_beta
13	234	InterPro	IPR012785	Protocatechuate 3,4-dioxygenase, beta subunit
11	240	SUPERFAMILY	SSF49482	Aromatic compound dioxygenase
11	240	InterPro	IPR015889	Intradiol ring-cleavage dioxygenase, core
42	238	PANTHER	PTHR33711	DIOXYGENASE, PUTATIVE (AFU_ORTHOLOGUE AFUA_2G02910)-RELATED
12	43	Pfam	PF12391	Protocatechuate 3,4-dioxygenase beta subunit N terminal
12	43	InterPro	IPR024756	Protocatechuate 3,4-dioxygenase beta subunit, N-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_A0A0H3GYR7	AlphaFold	—	—	full sequence	—	Viewing
ColabFold KP13_04442	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
4				0.135
8				0.028
12				0.004
1				0.0

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	7.94	0.356
2	5.0	0.187
3	1.37	0.014
4	1.35	0.013

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				3.7	0.141

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.

75 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
35C	3O32	O67987	179.0 Da LogP 2.40 TPSA 40.5	✓ Ro5	Alert	`c1c(cc(c(c1O)O)Cl)Cl`
3HB	3PCB	P00437	138.1 Da LogP 1.09 TPSA 57.5	✓ Ro5	✓ Clean	`c1cc(cc(c1)O)C(=O)O`
3HP	3PCE	P00437	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	1EOC	P20372	155.1 Da LogP 1.01 TPSA 83.6	✓ Ro5	Alert	`c1cc(c(cc1[N+](=O)[O-])O)O`
BEZ	1S9A	O67987	122.1 Da LogP 1.38 TPSA 37.3	✓ Ro5	✓ Clean	`c1ccc(cc1)C(=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	1EOB	P20371	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`
HGP	1S9A	O67987	707.0 Da LogP 10.46 TPSA 108.4	2 viol.	✓ Clean	`CCCCCCCCCCCCCCCC(=O)OC[C@H](CO[P@@](=O)(O)OCC[N…`
HQN	3O6J	O67987	126.1 Da LogP 0.80 TPSA 60.7	✓ Ro5	Alert	`c1cc(c(cc1O)O)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`
MYY	3O5U	O67987	620.8 Da LogP 9.73 TPSA 119.4	2 viol.	✓ Clean	`CCCCCCCCCCCCCCCC(=O)OC[C@H](COP(=O)(O)O)OC(=O)C…`
NNO	3PCK	P00437	155.1 Da LogP -0.28 TPSA 84.5	✓ Ro5	✓ Clean	`c1cc([n+](cc1C(=O)O)[O-])O`
PHB	2BUR	P20371	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…`
PYG	3O6R	O67987	126.1 Da LogP 0.80 TPSA 60.7	✓ Ro5	Alert	`c1cc(c(c(c1)O)O)O`
TAM	1S9A	O67987	163.2 Da LogP -1.17 TPSA 86.7	✓ Ro5	✓ Clean	`C(CO)C(CCO)(CCO)N`

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
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…`
ZINC13544781	1.000	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	1.000	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)…`
ZINC36178999	1.000	424.5 Da LogP 4.27 TPSA 119.4	✓ Ro5	✓ Clean	`CCCCCCCC(=O)OC[C@@H](COP(=O)(O)O)OC(=O)CCCCCCC`
ZINC36179002	1.000	424.5 Da LogP 4.27 TPSA 119.4	✓ Ro5	✓ Clean	`CCCCCCCC(=O)OC[C@H](COP(=O)(O)O)OC(=O)CCCCCCC`
ZINC13543439	0.977	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	0.977	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…`
ZINC5820131	0.971	368.4 Da LogP 2.71 TPSA 119.4	✓ Ro5	✓ Clean	`CCCCCC(=O)OC[C@@H](COP(=O)(O)O)OC(=O)CCCCC`
ZINC5820134	0.971	368.4 Da LogP 2.71 TPSA 119.4	✓ Ro5	✓ Clean	`CCCCCC(=O)OC[C@H](COP(=O)(O)O)OC(=O)CCCCC`
ZINC33822387	0.911	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	0.911	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)…`
ZINC389804	0.842	214.2 Da LogP 2.76 TPSA 57.5	✓ Ro5	✓ Clean	`O=C(O)c1ccc(-c2ccc(O)cc2)cc1`
ZINC12834352	0.826	398.4 Da LogP 1.88 TPSA 108.4	✓ Ro5	✓ Clean	`CCCC(=O)OC[C@@H](CO[P@](=O)(O)OCC[N+](C)(C)C)OC…`
ZINC12834353	0.826	398.4 Da LogP 1.88 TPSA 108.4	✓ Ro5	✓ Clean	`CCCC(=O)OC[C@H](CO[P@](=O)(O)OCC[N+](C)(C)C)OC(…`
ZINC32002933	0.786	228.2 Da LogP 2.69 TPSA 57.5	✓ Ro5	✓ Clean	`O=C(O)Cc1cccc(-c2cccc(O)c2)c1`
ZINC102190506	0.771	467.5 Da LogP 4.25 TPSA 134.4	✓ Ro5	✓ Clean	`CCCCCCCC(=O)OC[C@H](CO[P@@](=O)(O)OCCN)OC(=O)CC…`
ZINC102189757	0.755	454.6 Da LogP 4.04 TPSA 102.3	✓ Ro5	✓ Clean	`CCCCCCCCCCCCC(=O)OC[C@H](O)CO[P@@](=O)(O)OCC[N+…`
ZINC13544128	0.755	370.4 Da LogP 1.70 TPSA 102.3	✓ Ro5	✓ Clean	`CCCCCCC(=O)OC[C@@H](O)CO[P@](=O)(O)OCC[N+](C)(C…`
ZINC14880038	0.755	440.5 Da LogP 3.65 TPSA 102.3	✓ Ro5	✓ Clean	`CCCCCCCCCCCC(=O)OC[C@@H](O)CO[P@](=O)(O)OCC[N+]…`
ZINC14880039	0.755	440.5 Da LogP 3.65 TPSA 102.3	✓ Ro5	✓ Clean	`CCCCCCCCCCCC(=O)OC[C@H](O)CO[P@@](=O)(O)OCC[N+]…`
ZINC15297567	0.755	468.6 Da LogP 4.43 TPSA 102.3	✓ Ro5	✓ Clean	`CCCCCCCCCCCCCC(=O)OC[C@@H](O)CO[P@@](=O)(O)OCC[…`
ZINC32789157	0.755	412.5 Da LogP 2.87 TPSA 102.3	✓ Ro5	✓ Clean	`CCCCCCCCCC(=O)OC[C@@H](O)CO[P@](=O)(O)OCC[N+](C…`
ZINC32789161	0.755	412.5 Da LogP 2.87 TPSA 102.3	✓ Ro5	✓ Clean	`CCCCCCCCCC(=O)OC[C@H](O)CO[P@](=O)(O)OCC[N+](C)…`
ZINC32822149	0.755	468.6 Da LogP 4.43 TPSA 102.3	✓ Ro5	✓ Clean	`CCCCCCCCCCCCCC(=O)OC[C@H](O)CO[P@](=O)(O)OCC[N+…`
ZINC32822162	0.755	482.6 Da LogP 4.82 TPSA 102.3	✓ Ro5	✓ Clean	`CCCCCCCCCCCCCCC(=O)OC[C@@H](O)CO[P@@](=O)(O)OCC…`
ZINC32822163	0.755	482.6 Da LogP 4.82 TPSA 102.3	✓ Ro5	✓ Clean	`CCCCCCCCCCCCCCC(=O)OC[C@H](O)CO[P@](=O)(O)OCC[N…`
ZINC44305349	0.755	454.6 Da LogP 4.04 TPSA 102.3	✓ Ro5	✓ Clean	`CCCCCCCCCCCCC(=O)OC[C@@H](O)CO[P@@](=O)(O)OCC[N…`
ZINC44405718	0.755	398.5 Da LogP 2.48 TPSA 102.3	✓ Ro5	✓ Clean	`CCCCCCCCC(=O)OC[C@@H](O)CO[P@@](=O)(O)OCC[N+](C…`
ZINC44405722	0.755	426.5 Da LogP 3.26 TPSA 102.3	✓ Ro5	✓ Clean	`CCCCCCCCCCC(=O)OC[C@@H](O)CO[P@@](=O)(O)OCC[N+]…`
ZINC85576534	0.755	384.4 Da LogP 2.09 TPSA 102.3	✓ Ro5	✓ Clean	`CCCCCCCC(=O)OC[C@@H](O)CO[P@@](=O)(O)OCC[N+](C)…`
ZINC27416437	0.750	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	0.750	411.4 Da LogP 2.69 TPSA 134.4	✓ Ro5	✓ Clean	`CCCCCC(=O)OC[C@@H](CO[P@@](=O)(O)OCCN)OC(=O)CCC…`
ZINC4521879	0.743	386.5 Da LogP 4.73 TPSA 78.9	✓ Ro5	✓ Clean	`CCCCCC(=O)OCC(COC(=O)CCCCC)OC(=O)CCCCC`
ZINC13507210	0.735	356.4 Da LogP 1.31 TPSA 102.3	✓ Ro5	✓ Clean	`CCCCCC(=O)OC[C@@H](O)CO[P@](=O)(O)OCC[N+](C)(C)C`
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`
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`
ZINC102191119	0.711	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	0.711	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)…`
ZINC13508374	0.708	370.4 Da LogP 1.10 TPSA 108.4	✓ Ro5	✓ Clean	`CCC(=O)OC[C@H](CO[P@](=O)(O)OCC[N+](C)(C)C)OC(=…`
ZINC137999083	0.700	424.5 Da LogP 4.87 TPSA 113.3	✓ Ro5	✓ Clean	`CCCCCCCCCCCCCCCCC(=O)OC[C@H](O)COP(=O)(O)O`
ZINC42851452	0.700	424.5 Da LogP 4.87 TPSA 113.3	✓ Ro5	✓ Clean	`CCCCCCCCCCCCCCCCC(=O)OC[C@@H](O)COP(=O)(O)O`
ZINC62624856	0.700	382.4 Da LogP 3.70 TPSA 113.3	✓ Ro5	✓ Clean	`CCCCCCCCCCCCCC(=O)OC[C@H](O)COP(=O)(O)O`
ZINC62624861	0.700	382.4 Da LogP 3.70 TPSA 113.3	✓ Ro5	✓ Clean	`CCCCCCCCCCCCCC(=O)OC[C@@H](O)COP(=O)(O)O`
ZINC8218993	0.700	410.5 Da LogP 4.48 TPSA 113.3	✓ Ro5	✓ Clean	`CCCCCCCCCCCCCCCC(=O)OC[C@H](O)COP(=O)(O)O`
ZINC8219000	0.700	410.5 Da LogP 4.48 TPSA 113.3	✓ Ro5	✓ Clean	`CCCCCCCCCCCCCCCC(=O)OC[C@@H](O)COP(=O)(O)O`

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.