Protein profile

KP13_05249

Trans-aconitate 2-methyltransferase

Genome: KpKP13

Gene: tam AHE44655.1 Structure source: AlphaFold + ColabFold UniProt A0A0H3GN69

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Amino acids 253

Annotations 4

Features 11

PDB binders 1

Druggability 0.978

Overview

Basic information about this protein and its source genome.

Accession: KP13_05249
Assembly: Klebsiella pneumoniae subsp. pneumoniae Kp13, complete sequence
Gene: tam AHE44655.1
Status: annotated
Amino acids: 253
Structure source: AlphaFold + ColabFold

2.1.1.144

GO:0030798 Catalysis of the reaction: S-adenosyl-L-methionine + trans-aconitate = (E)-3-(methoxycarbonyl)pent-2-enedioate + S-adenosyl-L-homocysteine. GO:0005737 The contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures. GO:0032259 The process in which a methyl group is covalently attached to a molecule.

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: 94.02

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 0.978

Structure A0A0H3GN69

Pocket Pocket 1

P2Rank 0.957

Structure A0A0H3GN69

Pocket Pocket 1

ColabFold model

FPocket 0.53 · Pocket 2

P2Rank 0.983 · Pocket 1

Core conservation Accessory gene

Roary core

CoreCruncher accessory

Gut microbiome 73 / 4744 genomes with a hit

Normalized 0.015

Sequence

Primary amino-acid sequence viewer.

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 3 GO

Enzyme Commission (EC)

2.1.1.144

Gene Ontology (GO)

GO:0030798 Catalysis of the reaction: S-adenosyl-L-methionine + trans-aconitate = (E)-3-(methoxycarbonyl)pent-2-enedioate + S-adenosyl-L-homocysteine.
GO:0005737 The contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
GO:0032259 The process in which a methyl group is covalently attached to a molecule.

Sequence Features

Domain/signature hits from InterPro and related databases.

11 records

Show feature table

Start	End	DB	Term	Name
132	232	Gene3D	G3DSA:1.10.150.290	-
132	232	InterPro	IPR023149	Trans-aconitate 2-methyltransferase, C-terminal
3	245	PANTHER	PTHR43861	TRANS-ACONITATE 2-METHYLTRANSFERASE-RELATED
12	176	Pfam	PF13489	Methyltransferase domain
36	129	CDD	cd02440	AdoMet_MTases
19	239	SUPERFAMILY	SSF53335	S-adenosyl-L-methionine-dependent methyltransferases
19	239	InterPro	IPR029063	S-adenosyl-L-methionine-dependent methyltransferase superfamily
2	251	Hamap	MF_00560	Trans-aconitate 2-methyltransferase [tam].
2	251	InterPro	IPR023506	Trans-aconitate 2-methyltransferase
9	248	Gene3D	G3DSA:3.40.50.150	Vaccinia Virus protein VP39
9	248	InterPro	IPR029063	S-adenosyl-L-methionine-dependent methyltransferase superfamily

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_A0A0H3GN69	AlphaFold	—	—	full sequence	—	Viewing
ColabFold KP13_05249	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				0.978

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				27.78	0.922

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
2				0.53
12				0.327

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				38.47	0.96
2				1.23	0.012

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.

51 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
BEZ	3CCF	Q3MEY9	122.1 Da LogP 1.38 TPSA 37.3	✓ Ro5	✓ Clean	`c1ccc(cc1)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
ZINC3269660	0.824	254.2 Da LogP 2.45 TPSA 71.4	✓ Ro5	Alert	`O=C(O)c1ccc(C(=O)C(=O)c2ccccc2)cc1`
ZINC2504355	0.778	226.2 Da LogP 2.62 TPSA 54.4	✓ Ro5	✓ Clean	`O=C(O)c1ccc(C(=O)c2ccccc2)cc1`
ZINC1672966	0.688	210.2 Da LogP 2.75 TPSA 34.1	✓ Ro5	Alert	`O=C(C(=O)c1ccccc1)c1ccccc1`
ZINC34057267	0.684	274.3 Da LogP 4.72 TPSA 37.3	✓ Ro5	✓ Clean	`O=C(O)c1ccc(-c2ccc(-c3ccccc3)cc2)cc1`
ZINC114185151	0.647	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`
ZINC1590838	0.647	342.4 Da LogP 3.82 TPSA 68.3	✓ Ro5	Alert	`O=C(C(=O)c1ccc(C(=O)C(=O)c2ccccc2)cc1)c1ccccc1`
ZINC16133932	0.647	474.5 Da LogP 4.88 TPSA 102.4	✓ Ro5	Alert	`O=C(C(=O)c1ccc(C(=O)C(=O)c2ccc(C(=O)C(=O)c3cccc…`
ZINC1070912	0.611	286.3 Da LogP 4.15 TPSA 34.1	✓ Ro5	✓ Clean	`O=C(c1ccccc1)c1ccc(C(=O)c2ccccc2)cc1`
ZINC134079	0.611	242.2 Da LogP 2.75 TPSA 74.6	✓ Ro5	✓ Clean	`O=C(O)c1ccc(-c2ccc(C(=O)O)cc2)cc1`
ZINC1640789	0.611	374.3 Da LogP 3.55 TPSA 108.7	✓ Ro5	✓ Clean	`O=C(O)c1ccc(C(=O)c2ccc(C(=O)c3ccc(C(=O)O)cc3)cc…`
ZINC2146859	0.611	270.2 Da LogP 2.31 TPSA 91.7	✓ Ro5	✓ Clean	`O=C(O)c1ccc(C(=O)c2ccc(C(=O)O)cc2)cc1`
ZINC3147211	0.611	318.3 Da LogP 4.42 TPSA 74.6	✓ Ro5	✓ Clean	`O=C(O)c1ccc(-c2ccc(-c3ccc(C(=O)O)cc3)cc2)cc1`
ZINC2539781	0.600	382.1 Da LogP 4.24 TPSA 34.1	✓ Ro5	✓ Clean	`O=C(c1ccccc1)C(Br)(Br)C(=O)c1ccccc1`
ZINC100009533	0.591	226.2 Da LogP 3.80 TPSA 62.0	✓ Ro5	Alert	`O=C(O)c1ccc(/N=N\c2ccccc2)cc1`
ZINC12956625	0.591	226.2 Da LogP 3.80 TPSA 62.0	✓ Ro5	Alert	`O=C(O)c1ccc(N=Nc2ccccc2)cc1`
ZINC1601737	0.591	213.2 Da LogP 3.13 TPSA 49.3	✓ Ro5	✓ Clean	`O=C(O)c1ccc(Nc2ccccc2)cc1`
ZINC1689689	0.591	228.3 Da LogP 2.82 TPSA 61.4	✓ Ro5	✓ Clean	`O=C(O)c1ccc(NNc2ccccc2)cc1`
ZINC1697492	0.591	212.2 Da LogP 2.98 TPSA 37.3	✓ Ro5	✓ Clean	`O=C(O)c1ccc(Cc2ccccc2)cc1`
ZINC169818652	0.591	380.5 Da LogP 2.76 TPSA 37.3	✓ Ro5	✓ Clean	`O=C(O)c1ccc([Si](c2ccccc2)(c2ccccc2)c2ccccc2)cc1`
ZINC33759110	0.591	224.3 Da LogP 3.56 TPSA 37.3	✓ Ro5	✓ Clean	`O=C(O)c1ccc(/C=C/c2ccccc2)cc1`
ZINC346053	0.591	289.3 Da LogP 4.85 TPSA 40.5	✓ Ro5	✓ Clean	`O=C(O)c1ccc(N(c2ccccc2)c2ccccc2)cc1`
ZINC396612	0.591	230.3 Da LogP 3.54 TPSA 37.3	✓ Ro5	✓ Clean	`O=C(O)c1ccc(Sc2ccccc2)cc1`
ZINC409186	0.591	226.2 Da LogP 2.62 TPSA 54.4	✓ Ro5	✓ Clean	`O=C(O)c1cccc(C(=O)c2ccccc2)c1`
ZINC409394	0.591	226.3 Da LogP 3.17 TPSA 37.3	✓ Ro5	✓ Clean	`O=C(O)c1ccc(CCc2ccccc2)cc1`
ZINC4299335	0.591	222.2 Da LogP 2.78 TPSA 37.3	✓ Ro5	✓ Clean	`O=C(O)c1ccc(C#Cc2ccccc2)cc1`
ZINC4403618	0.591	226.2 Da LogP 3.80 TPSA 62.0	✓ Ro5	Alert	`O=C(O)c1ccc(/N=N/c2ccccc2)cc1`
ZINC4802802	0.591	288.3 Da LogP 4.57 TPSA 37.3	✓ Ro5	✓ Clean	`O=C(O)c1ccc(C(c2ccccc2)c2ccccc2)cc1`
ZINC5538754	0.591	304.3 Da LogP 3.67 TPSA 57.5	✓ Ro5	✓ Clean	`O=C(O)c1ccc(C(O)(c2ccccc2)c2ccccc2)cc1`
ZINC60939	0.591	214.2 Da LogP 3.18 TPSA 46.5	✓ Ro5	✓ Clean	`O=C(O)c1ccc(Oc2ccccc2)cc1`
ZINC254583	0.583	242.2 Da LogP 2.60 TPSA 63.6	✓ Ro5	✓ Clean	`O=C(O)c1ccc(OC(=O)c2ccccc2)cc1`
ZINC43214128	0.583	240.3 Da LogP 2.81 TPSA 54.4	✓ Ro5	✓ Clean	`O=C(O)c1ccc(CC(=O)c2ccccc2)cc1`
ZINC78349	0.583	241.2 Da LogP 2.64 TPSA 66.4	✓ Ro5	✓ Clean	`O=C(O)c1ccc(NC(=O)c2ccccc2)cc1`
ZINC1718650	0.579	238.2 Da LogP 2.32 TPSA 51.2	✓ Ro5	Alert	`O=C(C(=O)c1ccccc1)C(=O)c1ccccc1`
ZINC4530702	0.579	224.3 Da LogP 3.14 TPSA 34.1	✓ Ro5	✓ Clean	`O=C(CC(=O)c1ccccc1)c1ccccc1`
ZINC96315996	0.579	268.3 Da LogP 2.77 TPSA 74.6	✓ Ro5	✓ Clean	`O=C(O)/C(=C(\C(=O)O)c1ccccc1)c1ccccc1`
ZINC1496851	0.571	260.2 Da LogP 3.39 TPSA 34.1	✓ Ro5	✓ Clean	`O=C(c1ccccc1)C(F)(F)C(=O)c1ccccc1`
ZINC1602461	0.571	223.5 Da LogP 3.24 TPSA 17.1	✓ Ro5	✓ Clean	`O=C(c1ccccc1)C(Cl)(Cl)Cl`
ZINC1726772	0.571	252.3 Da LogP 3.78 TPSA 34.1	✓ Ro5	✓ Clean	`CC(C)(C(=O)c1ccccc1)C(=O)c1ccccc1`
ZINC207916	0.571	270.2 Da LogP 2.31 TPSA 91.7	✓ Ro5	✓ Clean	`O=C(O)c1cccc(C(=O)c2cccc(C(=O)O)c2)c1`
ZINC21298253	0.571	358.3 Da LogP 0.38 TPSA 149.2	✓ Ro5	✓ Clean	`O=C(O)[C@@](O)(C(=O)c1ccccc1)[C@@](O)(C(=O)O)C(…`
ZINC21298260	0.571	358.3 Da LogP 0.38 TPSA 149.2	✓ Ro5	✓ Clean	`O=C(O)[C@@](O)(C(=O)c1ccccc1)[C@](O)(C(=O)O)C(=…`
ZINC21298267	0.571	358.3 Da LogP 0.38 TPSA 149.2	✓ Ro5	✓ Clean	`O=C(O)[C@](O)(C(=O)c1ccccc1)[C@](O)(C(=O)O)C(=O…`
ZINC3897007	0.571	242.2 Da LogP 2.75 TPSA 74.6	✓ Ro5	✓ Clean	`O=C(O)c1cccc(-c2cccc(C(=O)O)c2)c1`
ZINC1670917	0.565	228.2 Da LogP 2.47 TPSA 57.5	✓ Ro5	✓ Clean	`O=C(O)c1ccc([C@@H](O)c2ccccc2)cc1`
ZINC2043250	0.565	228.2 Da LogP 2.47 TPSA 57.5	✓ Ro5	✓ Clean	`O=C(O)c1ccc([C@H](O)c2ccccc2)cc1`
ZINC289040	0.565	262.3 Da LogP 2.22 TPSA 71.4	✓ Ro5	✓ Clean	`O=C(O)c1ccc(S(=O)(=O)c2ccccc2)cc1`
ZINC394370	0.565	270.2 Da LogP 2.31 TPSA 91.7	✓ Ro5	✓ Clean	`O=C(O)c1ccc(C(=O)c2ccccc2C(=O)O)cc1`
ZINC6624011	0.565	258.3 Da LogP 2.15 TPSA 77.8	✓ Ro5	✓ Clean	`O=C(O)c1ccc([C@@H](O)[C@H](O)c2ccccc2)cc1`
ZINC6624012	0.565	258.3 Da LogP 2.15 TPSA 77.8	✓ Ro5	✓ Clean	`O=C(O)c1ccc([C@H](O)[C@@H](O)c2ccccc2)cc1`
ZINC6624013	0.565	258.3 Da LogP 2.15 TPSA 77.8	✓ Ro5	✓ Clean	`O=C(O)c1ccc([C@H](O)[C@H](O)c2ccccc2)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.