Protein profile

PA2009

homogentisate 1,2-dioxygenase

Genome: NC_002516.2

Gene: PA2009 hmgA Structure source: AlphaFold UniProt Q9X4G0

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Amino acids 432

Annotations 6

Features 16

PDB binders 6

Druggability 0.643

Overview

Basic information about this protein and its source genome.

Accession: PA2009
Assembly: Pseudomonas aeruginosa PAO1, complete genome
Gene: PA2009 hmgA
Status: annotated
Amino acids: 432
Structure source: AlphaFold

1.13.11.5

GO:0004411 Catalysis of the reaction: homogentisate + O2 = 4-maleylacetoacetate + H+. GO:0005506 Binding to an iron (Fe) ion. GO:0006559 The chemical reactions and pathways resulting in the breakdown of L-phenylalanine. GO:0006572 The chemical reactions and pathways resulting in the breakdown of L-tyrosine. GO:0006570 The chemical reactions and pathways involving tyrosine, an aromatic amino acid, 2-amino-3-(4-hydroxyphenyl)propanoic acid.

Target profile

Computed evidence for target prioritization.

Human off-target: hit
Human identity (%): 60.563
Human E-value: 4.450000000000001e-56
Gut microbiome off-target: hit
Essential (DEG): N
Localization: Unknown

Selected Druggability evidence

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 0.643

Structure –

Pocket –

Sequence

Primary amino-acid sequence viewer.

MNLDSTALAYQSGFGNEFSSEALPGALPVGQNSPQKAPYGLYAELLSGTAFTMARSEARRTWLYRITPSAKHPPFRRLERQIAGAELDAPTPNRLRWDPLALPEQPTDFLDGLLRMAANAPGDKPAGVSIYQYLANRSMERCFYDADGELLLVPQLGRLRLCTELGALQVEPLEIAVIPRGMKFRVELLDGEARGYIAENHGAPLRLPDLGPIGSNGLANPRDFLTPVARYEDSRQPLQLVQKYLGELWACELDHSPLDVVAWHGNNVPYKYDLRRFNTIGTVSFDHPDPSIFTVLTSPTSVPGLANIDFVIFPPRWMVAENTFRPPWFHRNLMNEFMGLIQGAYDAKAGGFVPGGASLHSCMSAHGPDAESCDKAIAADLKPHRIDQTMAFMFETSQVLRPSRAALETPALQNDYDACWASLVSTFNPQRR

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 5 GO

Enzyme Commission (EC)

1.13.11.5

Gene Ontology (GO)

GO:0004411 Catalysis of the reaction: homogentisate + O2 = 4-maleylacetoacetate + H+.
GO:0005506 Binding to an iron (Fe) ion.
GO:0006559 The chemical reactions and pathways resulting in the breakdown of L-phenylalanine.
GO:0006572 The chemical reactions and pathways resulting in the breakdown of L-tyrosine.
GO:0006570 The chemical reactions and pathways involving tyrosine, an aromatic amino acid, 2-amino-3-(4-hydroxyphenyl)propanoic acid.

Sequence Features

Domain/signature hits from InterPro and related databases.

16 records

Show feature table

Start	End	DB	Term	Name
95	202	CDD	cd07000	cupin_HGO_N
9	429	Hamap	MF_00334	Homogentisate 1,2-dioxygenase [hmgA].
9	429	InterPro	IPR022950	Homogentisate 1,2-dioxygenase, bacterial
265	398	FunFam	G3DSA:2.60.120.10:FF:000036	Homogentisate 1,2-dioxygenase
6	430	PANTHER	PTHR11056	HOMOGENTISATE 1,2-DIOXYGENASE
6	430	InterPro	IPR005708	Homogentisate 1,2-dioxygenase
275	427	Pfam	PF04209	Homogentisate 1,2-dioxygenase C-terminal
275	427	InterPro	IPR046451	Homogentisate 1,2-dioxygenase, C-terminal domain
9	274	Pfam	PF20510	Homogentisate 1,2-dioxygenase N-terminal
9	274	InterPro	IPR046452	Homogentisate 1,2-dioxygenase, N-terminal domain
273	398	Gene3D	G3DSA:2.60.120.10	Jelly Rolls
273	398	InterPro	IPR014710	RmlC-like jelly roll fold
8	426	NCBIfam	TIGR01015	homogentisate 1,2-dioxygenase
8	426	InterPro	IPR005708	Homogentisate 1,2-dioxygenase
8	431	SUPERFAMILY	SSF51182	RmlC-like cupins
8	431	InterPro	IPR011051	RmlC-like cupin domain superfamily

3D Structure

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

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Structural evidence

0 + 1

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

Entry	Method	Resolution	Chain	Coverage	Links	Status
AlphaFold PA2009	AlphaFold	—	—	full sequence	—	Viewing

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
3				0.643
1				0.571

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.

36 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
B3P	4AQ2	Q88E47	282.3 Da LogP -4.01 TPSA 145.4	1 viol.	✓ Clean	`C(CNC(CO)(CO)CO)CNC(CO)(CO)CO`
HMQ	3ZDS	Q88E47	200.1 Da LogP -0.30 TPSA 104.1	✓ Ro5	✓ Clean	`C1=C[C@@](C(=CC1=O)CC(=O)O)(O)OO`
HQ9	3ZDS	Q88E47	168.1 Da LogP -0.11 TPSA 74.6	✓ Ro5	✓ Clean	`C1=CC(=O)C=C([C@H]1O)CC(=O)O`
M8O	3ZDS	Q88E47	200.1 Da LogP -0.37 TPSA 108.7	✓ Ro5	✓ Clean	`C(C(=O)CC(=O)O)C(=O)C=CC(=O)O`
OMD	3ZDS	Q88E47	168.1 Da LogP 0.72 TPSA 77.8	✓ Ro5	✓ Clean	`c1cc(c(cc1O)CC(=O)O)O`
OXY	3ZDS	Q88E47	32.0 Da LogP 0.07 TPSA 34.1	✓ Ro5	✓ Clean	`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
ZINC4521259	1.000	282.3 Da LogP -4.01 TPSA 145.4	1 viol.	✓ Clean	`OCC(CO)(CO)NCCCNC(CO)(CO)CO`
ZINC1231942	0.679	255.2 Da LogP 0.07 TPSA 118.3	✓ Ro5	Alert	`O=C(O)CN(CC(=O)O)Cc1cc(O)ccc1O`
ZINC1673662	0.640	260.3 Da LogP 2.68 TPSA 80.9	✓ Ro5	✓ Clean	`Oc1ccc(O)c(CCCc2cc(O)ccc2O)c1`
ZINC115591405	0.636	373.6 Da LogP 4.55 TPSA 72.7	✓ Ro5	✓ Clean	`CCCCCCCCCCCCCCCCCCNC(CO)(CO)CO`
ZINC115591837	0.636	317.5 Da LogP 2.99 TPSA 72.7	✓ Ro5	✓ Clean	`CCCCCCCCCCCCCCNC(CO)(CO)CO`
ZINC143575268	0.636	289.5 Da LogP 2.21 TPSA 72.7	✓ Ro5	✓ Clean	`CCCCCCCCCCCCNC(CO)(CO)CO`
ZINC2322313	0.636	233.4 Da LogP 0.65 TPSA 72.7	✓ Ro5	✓ Clean	`CCCCCCCCNC(CO)(CO)CO`
ZINC97996983	0.636	345.6 Da LogP 3.77 TPSA 72.7	✓ Ro5	✓ Clean	`CCCCCCCCCCCCCCCCNC(CO)(CO)CO`
ZINC66325507	0.630	231.0 Da LogP 1.78 TPSA 57.5	✓ Ro5	✓ Clean	`O=C(O)Cc1cc(Br)ccc1O`
ZINC84511682	0.630	231.0 Da LogP 1.78 TPSA 57.5	✓ Ro5	✓ Clean	`O=C(O)Cc1cc(O)ccc1Br`
ZINC1673681	0.615	288.3 Da LogP 3.46 TPSA 80.9	✓ Ro5	✓ Clean	`Oc1ccc(O)c(CCCCCc2cc(O)ccc2O)c1`
ZINC404362	0.609	226.2 Da LogP 0.35 TPSA 115.1	✓ Ro5	✓ Clean	`O=C(O)Cc1cc(O)c(CC(=O)O)cc1O`
ZINC1673678	0.594	211.2 Da LogP 0.44 TPSA 103.8	✓ Ro5	✓ Clean	`N[C@H](CCc1cc(O)ccc1O)C(=O)O`
ZINC6511462	0.594	211.2 Da LogP 0.44 TPSA 103.8	✓ Ro5	✓ Clean	`N[C@@H](CCc1cc(O)ccc1O)C(=O)O`
ZINC1611594	0.583	243.3 Da LogP -2.43 TPSA 127.1	✓ Ro5	✓ Clean	`O=S(=O)(O)CCCNC(CO)(CO)CO`
ZINC5273895	0.583	257.3 Da LogP -2.04 TPSA 127.1	✓ Ro5	✓ Clean	`O=S(=O)(O)CCCCNC(CO)(CO)CO`
ZINC1634585	0.576	274.3 Da LogP 2.29 TPSA 98.0	✓ Ro5	✓ Clean	`O=C(O)c1cc(CCc2cc(O)ccc2O)ccc1O`
ZINC83072634	0.571	231.0 Da LogP 1.78 TPSA 57.5	✓ Ro5	✓ Clean	`O=C(O)Cc1ccc(O)cc1Br`
ZINC1654161	0.567	222.3 Da LogP 4.00 TPSA 40.5	✓ Ro5	✓ Clean	`CCCCCCCCc1cc(O)ccc1O`
ZINC1654158	0.552	200.2 Da LogP 2.69 TPSA 40.5	✓ Ro5	✓ Clean	`Oc1ccc(O)c(Cc2ccccc2)c1`
ZINC13306196	0.533	210.2 Da LogP 0.93 TPSA 94.8	✓ Ro5	✓ Clean	`CC(=O)c1c(O)cc(O)cc1CC(=O)O`
ZINC33604885	0.533	202.2 Da LogP 2.17 TPSA 57.5	✓ Ro5	✓ Clean	`O=C(O)Cc1ccc2cc(O)ccc2c1`
ZINC1857793	0.528	272.3 Da LogP 2.67 TPSA 66.8	✓ Ro5	✓ Clean	`COC(=O)c1ccc(CCc2cc(O)ccc2O)cc1`
ZINC108313765	0.517	202.2 Da LogP 2.17 TPSA 57.5	✓ Ro5	✓ Clean	`O=C(O)Cc1cc2ccccc2cc1O`
ZINC169796979	0.516	220.1 Da LogP 2.04 TPSA 57.5	✓ Ro5	✓ Clean	`O=C(O)Cc1ccc(O)cc1C(F)(F)F`
ZINC1530141	0.500	229.3 Da LogP -2.82 TPSA 127.1	✓ Ro5	✓ Clean	`O=S(=O)(O)CCNC(CO)(CO)CO`
ZINC1651674	0.500	257.3 Da LogP 2.91 TPSA 69.6	✓ Ro5	Alert	`CC(=O)c1ccc(NCc2cc(O)ccc2O)cc1`
ZINC388549	0.500	275.3 Da LogP 2.11 TPSA 110.0	✓ Ro5	Alert	`O=C(O)c1cc(NCc2cc(O)ccc2O)ccc1O`
ZINC84556694	0.500	245.1 Da LogP 2.17 TPSA 57.5	✓ Ro5	✓ Clean	`O=C(O)CCc1cc(O)ccc1Br`
ZINC968695	0.500	255.2 Da LogP 0.07 TPSA 118.3	✓ Ro5	Alert	`O=C(O)CN(CC(=O)O)Cc1ccc(O)cc1O`

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.