Protein profile

PA1927

5-methyltetrahydropteroyltriglutamate-- homocysteine methyltransferase

Genome: NC_002516.2

Gene: metE PA1927 Structure source: AlphaFold UniProt P57703

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Amino acids 766

Annotations 7

Features 24

PDB binders 6

Druggability 0.647

Overview

Basic information about this protein and its source genome.

Accession: PA1927
Assembly: Pseudomonas aeruginosa PAO1, complete genome
Gene: metE PA1927
Status: annotated
Amino acids: 766
Structure source: AlphaFold

2.1.1.14

GO:0003871 Catalysis of the reaction: 5-methyltetrahydropteroyltri-L-glutamate + L-homocysteine = L-methionine + tetrahydropteroyltri-L-glutamate. GO:0008270 Binding to a zinc ion (Zn). GO:0071265 The chemical reactions and pathways resulting in the formation of L-methionine, the L-enantiomer of (2S)-2-amino-4-(methylsulfanyl)butanoic acid. GO:0032259 The process in which a methyl group is covalently attached to a molecule. GO:0008652 The chemical reactions and pathways resulting in the formation of amino acids, organic acids containing one or more amino substituents. GO:0009086 OBSOLETE. The chemical reactions and pathways resulting in the de novo formation of L-methionine (2-amino-4-(methylthio)butanoic acid), a sulfur-containing, essential amino acid found in peptide linkage in proteins.

Target profile

Computed evidence for target prioritization.

Human off-target: No hit
Gut microbiome off-target: hit
Essential (DEG): Y
Localization: Cytoplasmic

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 0.647

Structure –

Pocket –

Sequence

Primary amino-acid sequence viewer.

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 6 GO

Enzyme Commission (EC)

2.1.1.14

Gene Ontology (GO)

GO:0003871 Catalysis of the reaction: 5-methyltetrahydropteroyltri-L-glutamate + L-homocysteine = L-methionine + tetrahydropteroyltri-L-glutamate.
GO:0008270 Binding to a zinc ion (Zn).
GO:0071265 The chemical reactions and pathways resulting in the formation of L-methionine, the L-enantiomer of (2S)-2-amino-4-(methylsulfanyl)butanoic acid.
GO:0032259 The process in which a methyl group is covalently attached to a molecule.
GO:0008652 The chemical reactions and pathways resulting in the formation of amino acids, organic acids containing one or more amino substituents.
GO:0009086 OBSOLETE. The chemical reactions and pathways resulting in the de novo formation of L-methionine (2-amino-4-(methylthio)butanoic acid), a sulfur-containing, essential amino acid found in peptide linkage in proteins.

Sequence Features

Domain/signature hits from InterPro and related databases.

24 records

Show feature table

Start	End	DB	Term	Name
395	760	FunFam	G3DSA:3.20.20.210:FF:000002	5-methyltetrahydropteroyltriglutamate--homocysteine methyltransferase
400	761	SUPERFAMILY	SSF51726	UROD/MetE-like
400	761	InterPro	IPR038071	UROD/MetE-like superfamily
436	758	CDD	cd03311	CIMS_C_terminal_like
436	758	InterPro	IPR002629	Cobalamin-independent methionine synthase MetE, C-terminal/archaeal
393	760	Gene3D	G3DSA:3.20.20.210	-
393	760	InterPro	IPR038071	UROD/MetE-like superfamily
6	528	Gene3D	G3DSA:3.20.20.210	-
6	528	InterPro	IPR038071	UROD/MetE-like superfamily
435	757	Pfam	PF01717	Cobalamin-independent synthase, Catalytic domain
435	757	InterPro	IPR002629	Cobalamin-independent methionine synthase MetE, C-terminal/archaeal
7	760	NCBIfam	TIGR01371	5-methyltetrahydropteroyltriglutamate--homocysteine S-methyltransferase
7	760	InterPro	IPR006276	Cobalamin-independent methionine synthase
3	398	SUPERFAMILY	SSF51726	UROD/MetE-like
3	398	InterPro	IPR038071	UROD/MetE-like superfamily
4	764	PANTHER	PTHR30519	5-METHYLTETRAHYDROPTEROYLTRIGLUTAMATE--HOMOCYSTEINE METHYLTRANSFERASE
6	394	FunFam	G3DSA:3.20.20.210:FF:000003	5-methyltetrahydropteroyltriglutamate--homocysteine methyltransferase
3	367	CDD	cd03312	CIMS_N_terminal_like
1	765	PIRSF	PIRSF000382	Met_synth_MetE
1	765	InterPro	IPR006276	Cobalamin-independent methionine synthase
4	317	Pfam	PF08267	Cobalamin-independent synthase, N-terminal domain
4	317	InterPro	IPR013215	Cobalamin-independent methionine synthase MetE, N-terminal
2	762	Hamap	MF_00172	5-methyltetrahydropteroyltriglutamate--homocysteine methyltransferase [metE].
2	762	InterPro	IPR006276	Cobalamin-independent methionine synthase

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 PA1927	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
1				0.646

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.

56 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
39S	4QQU	P82610	703.7 Da LogP -1.58 TPSA 344.4	3 viol.	✓ Clean	`c1cc(ccc1C(=O)N[C@@H](CCC(=O)N[C@@H](CCC(=O)N[C…`
C2F	1U1J	O50008	459.5 Da LogP -0.26 TPSA 202.8	1 viol.	✓ Clean	`C[N@@]1[C@H](CNC2=C1C(=O)NC(=N2)N)CNc3ccc(cc3)C…`
HCS	1U22	O50008	135.2 Da LogP -0.28 TPSA 63.3	✓ Ro5	✓ Clean	`C(CS)[C@@H](C(=O)O)N`
MRY	1T7L	Q9X112	122.1 Da LogP -2.31 TPSA 80.9	✓ Ro5	✓ Clean	`C([C@H]([C@H](CO)O)O)O`
MTX	4L6H	P82610	454.4 Da LogP 0.27 TPSA 210.5	✓ Ro5	✓ Clean	`CN(Cc1cnc2c(n1)c(nc(n2)N)N)c3ccc(cc3)C(=O)N[C@@…`
THG	1U22	O50008	445.4 Da LogP -0.28 TPSA 211.6	1 viol.	✓ Clean	`c1cc(ccc1C(=O)N[C@@H](CCC(=O)O)C(=O)O)NC[C@H]2C…`

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
ZINC2005305	1.000	459.5 Da LogP -0.26 TPSA 202.8	1 viol.	✓ Clean	`CN1c2c(nc(N)[nH]c2=O)NC[C@@H]1CNc1ccc(C(=O)N[C@…`
ZINC2572666	1.000	459.5 Da LogP -0.26 TPSA 202.8	1 viol.	✓ Clean	`CN1c2c(nc(N)[nH]c2=O)NC[C@H]1CNc1ccc(C(=O)N[C@@…`
ZINC4228266	1.000	459.5 Da LogP -0.26 TPSA 202.8	1 viol.	✓ Clean	`CN1c2c(nc(N)[nH]c2=O)NC[C@@H]1CNc1ccc(C(=O)N[C@…`
ZINC4228267	1.000	459.5 Da LogP -0.26 TPSA 202.8	1 viol.	✓ Clean	`CN1c2c(nc(N)[nH]c2=O)NC[C@H]1CNc1ccc(C(=O)N[C@H…`
ZINC13604299	0.825	439.5 Da LogP 0.14 TPSA 199.3	✓ Ro5	✓ Clean	`CN(Cc1cnc2nc(N)nc(N)c2n1)c1ccc(C(=O)N[C@@H](CCC…`
ZINC13284373	0.813	453.5 Da LogP 0.53 TPSA 199.3	✓ Ro5	✓ Clean	`CN(Cc1cnc2nc(N)nc(N)c2n1)c1ccc(C(=O)N[C@@H](CCC…`
ZINC8627939	0.813	453.5 Da LogP 0.53 TPSA 199.3	✓ Ro5	✓ Clean	`CN(Cc1cnc2nc(N)nc(N)c2n1)c1ccc(C(=O)N[C@H](CCCC…`
ZINC9212425	0.803	473.4 Da LogP -0.73 TPSA 219.8	1 viol.	✓ Clean	`Nc1nc2c(c(=O)[nH]1)N(C=O)[C@@H](CNc1ccc(C(=O)N[…`
ZINC9212426	0.803	473.4 Da LogP -0.73 TPSA 219.8	1 viol.	✓ Clean	`Nc1nc2c(c(=O)[nH]1)N(C=O)[C@H](CNc1ccc(C(=O)N[C…`
ZINC9212427	0.803	473.4 Da LogP -0.73 TPSA 219.8	1 viol.	✓ Clean	`Nc1nc2c(c(=O)[nH]1)N(C=O)[C@@H](CNc1ccc(C(=O)N[…`
ZINC9212428	0.803	473.4 Da LogP -0.73 TPSA 219.8	1 viol.	✓ Clean	`Nc1nc2c(c(=O)[nH]1)N(C=O)[C@H](CNc1ccc(C(=O)N[C…`
ZINC255970296	0.794	478.5 Da LogP 0.05 TPSA 226.7	✓ Ro5	Alert	`CN(Cc1cnc2nc(N)nc(N)c2n1)c1ccc(C(=O)N[C@@H](CCC…`
ZINC22062147	0.785	482.5 Da LogP 0.45 TPSA 188.5	1 viol.	✓ Clean	`COC(=O)CC[C@H](NC(=O)c1ccc(N(C)Cc2cnc3nc(N)nc(N…`
ZINC1734471	0.765	488.9 Da LogP 0.92 TPSA 210.5	✓ Ro5	✓ Clean	`CN(Cc1cnc2nc(N)nc(N)c2n1)c1ccc(C(=O)N[C@@H](CCC…`
ZINC8628726	0.765	488.9 Da LogP 0.92 TPSA 210.5	✓ Ro5	✓ Clean	`CN(Cc1cnc2nc(N)nc(N)c2n1)c1ccc(C(=O)N[C@H](CCC(…`
ZINC98207756	0.727	330.3 Da LogP 0.39 TPSA 136.4	✓ Ro5	✓ Clean	`CN1c2c(nc(N)[nH]c2=O)NC[C@@H]1CNc1ccc(C(=O)O)cc1`
ZINC1560410190	0.712	453.4 Da LogP 0.43 TPSA 210.5	✓ Ro5	✓ Clean	`CN(Cc1cnc2nc(N)nc(N)c2n1)c1ccc(C(=O)N[C](CCC(=O…`
ZINC8655682	0.711	487.5 Da LogP -0.34 TPSA 219.8	1 viol.	✓ Clean	`Nc1nc2c(c(=O)[nH]1)N(C=O)[C@@H](CCNc1ccc(C(=O)N…`
ZINC4228235	0.708	445.4 Da LogP -0.28 TPSA 211.6	1 viol.	✓ Clean	`Nc1nc2c(c(=O)[nH]1)N[C@H](CNc1ccc(C(=O)N[C@@H](…`
ZINC4228236	0.708	445.4 Da LogP -0.28 TPSA 211.6	1 viol.	✓ Clean	`Nc1nc2c(c(=O)[nH]1)N[C@H](CNc1ccc(C(=O)N[C@H](C…`
ZINC4228237	0.708	445.4 Da LogP -0.28 TPSA 211.6	1 viol.	✓ Clean	`Nc1nc2c(c(=O)[nH]1)N[C@@H](CNc1ccc(C(=O)N[C@@H]…`
ZINC4228238	0.708	445.4 Da LogP -0.28 TPSA 211.6	1 viol.	✓ Clean	`Nc1nc2c(c(=O)[nH]1)N[C@@H](CNc1ccc(C(=O)N[C@H](…`
ZINC404265	0.683	325.3 Da LogP 0.92 TPSA 144.1	✓ Ro5	✓ Clean	`CN(Cc1cnc2nc(N)nc(N)c2n1)c1ccc(C(=O)O)cc1`
ZINC8628600	0.671	473.5 Da LogP 0.13 TPSA 202.8	1 viol.	✓ Clean	`CN1c2c([nH]c(N)nc2=O)NC[C@@H]1CCNc1ccc(C(=O)N[C…`
ZINC8628601	0.671	473.5 Da LogP 0.13 TPSA 202.8	1 viol.	✓ Clean	`CN1c2c([nH]c(N)nc2=O)NC[C@H]1CCNc1ccc(C(=O)N[C@…`
ZINC1720422	0.651	339.4 Da LogP 1.01 TPSA 133.1	✓ Ro5	✓ Clean	`COC(=O)c1ccc(N(C)Cc2cnc3nc(N)nc(N)c3n2)cc1`
ZINC4228243	0.645	457.4 Da LogP -0.52 TPSA 194.0	1 viol.	✓ Clean	`Nc1nc2c(c(=O)[nH]1)N1CN(c3ccc(C(=O)N[C@@H](CCC(…`
ZINC4228244	0.645	457.4 Da LogP -0.52 TPSA 194.0	1 viol.	✓ Clean	`Nc1nc2c(c(=O)[nH]1)N1CN(c3ccc(C(=O)N[C@H](CCC(=…`
ZINC4654260	0.645	457.4 Da LogP -0.52 TPSA 194.0	1 viol.	✓ Clean	`Nc1nc2c(c(=O)[nH]1)N1CN(c3ccc(C(=O)N[C@@H](CCC(…`
ZINC8618631	0.645	459.5 Da LogP 0.11 TPSA 211.6	1 viol.	✓ Clean	`Nc1nc2c(c(=O)[nH]1)N[C@H](CCNc1ccc(C(=O)N[C@@H]…`
ZINC8627114	0.645	459.5 Da LogP 0.11 TPSA 211.6	1 viol.	✓ Clean	`Nc1nc2c(c(=O)[nH]1)N[C@@H](CCNc1ccc(C(=O)N[C@@H…`
ZINC4654270	0.632	471.4 Da LogP -0.36 TPSA 211.0	1 viol.	✓ Clean	`Nc1nc2c(c(=O)[nH]1)N1C(=O)N(c3ccc(C(=O)N[C@@H](…`
ZINC4654271	0.632	471.4 Da LogP -0.36 TPSA 211.0	1 viol.	✓ Clean	`Nc1nc2c(c(=O)[nH]1)N1C(=O)N(c3ccc(C(=O)N[C@@H](…`
ZINC3055005	0.619	204.2 Da LogP -0.63 TPSA 126.6	✓ Ro5	✓ Clean	`N[C@@H](CCCC[C@H](N)C(=O)O)C(=O)O`
ZINC3055007	0.619	204.2 Da LogP -0.63 TPSA 126.6	✓ Ro5	✓ Clean	`N[C@@H](CCCC[C@@H](N)C(=O)O)C(=O)O`
ZINC3055010	0.619	204.2 Da LogP -0.63 TPSA 126.6	✓ Ro5	✓ Clean	`N[C@H](CCCC[C@@H](N)C(=O)O)C(=O)O`
ZINC100055463	0.615	212.2 Da LogP -4.22 TPSA 141.6	1 viol.	✓ Clean	`OC[C@H](O)[C@@H](O)[C@H](O)[C@H](O)[C@H](O)CO`
ZINC100064885	0.615	212.2 Da LogP -4.22 TPSA 141.6	1 viol.	✓ Clean	`OC[C@H](O)[C@@H](O)[C@@H](O)[C@H](O)[C@H](O)CO`
ZINC1653968	0.615	353.4 Da LogP 1.40 TPSA 133.1	✓ Ro5	✓ Clean	`CCOC(=O)c1ccc(N(C)Cc2cnc3nc(N)nc(N)c3n2)cc1`
ZINC17780060	0.615	212.2 Da LogP -4.22 TPSA 141.6	1 viol.	✓ Clean	`OC[C@@H](O)[C@H](O)C(O)[C@H](O)[C@H](O)CO`
ZINC17952732	0.615	212.2 Da LogP -4.22 TPSA 141.6	1 viol.	✓ Clean	`OC[C@H](O)[C@@H](O)C(O)[C@H](O)[C@H](O)CO`
ZINC18042331	0.615	242.2 Da LogP -4.86 TPSA 161.8	1 viol.	✓ Clean	`OC[C@H](O)[C@H](O)[C@H](O)[C@H](O)[C@H](O)[C@H]…`
ZINC18120313	0.615	212.2 Da LogP -4.22 TPSA 141.6	1 viol.	✓ Clean	`OC[C@H](O)[C@H](O)C(O)[C@H](O)[C@H](O)CO`
ZINC3979006	0.615	212.2 Da LogP -4.22 TPSA 141.6	1 viol.	✓ Clean	`OC[C@@H](O)[C@@H](O)C(O)[C@H](O)[C@H](O)CO`
ZINC4403103	0.615	242.2 Da LogP -4.86 TPSA 161.8	1 viol.	✓ Clean	`OC[C@@H](O)[C@H](O)[C@H](O)[C@H](O)[C@H](O)[C@H…`
ZINC4403105	0.615	242.2 Da LogP -4.86 TPSA 161.8	1 viol.	✓ Clean	`OC[C@H](O)[C@@H](O)[C@H](O)[C@H](O)[C@H](O)[C@H…`
ZINC4403107	0.615	242.2 Da LogP -4.86 TPSA 161.8	1 viol.	✓ Clean	`OC[C@@H](O)[C@@H](O)[C@H](O)[C@H](O)[C@H](O)[C@…`
ZINC9212412	0.615	212.2 Da LogP -4.22 TPSA 141.6	1 viol.	✓ Clean	`OC[C@H](O)[C@@H](O)C(O)[C@H](O)[C@@H](O)CO`
ZINC4228265	0.605	443.4 Da LogP 0.01 TPSA 211.9	1 viol.	✓ Clean	`Nc1nc2c(c(=O)[nH]1)N=C(CNc1ccc(C(=O)N[C@@H](CCC…`
ZINC4658144	0.605	443.5 Da LogP 0.62 TPSA 187.5	1 viol.	✓ Clean	`Nc1nc2c(c(=O)[nH]1)C[C@@H](CCc1ccc(C(=O)N[C@H](…`

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.