Protein profile

PA5215

glycine cleavage system aminomethyltransferase T

Genome: NC_002516.2

Gene: gcvT1 Structure source: ColabFold

Export view

Amino acids 360

Annotations 3

Features 22

PDB binders 5

Druggability 0.879

Overview

Basic information about this protein and its source genome.

Accession: PA5215
Assembly: Pseudomonas aeruginosa PAO1, complete genome
Gene: gcvT1
Status: annotated
Amino acids: 360
Structure source: ColabFold

GO:0006546 The chemical reactions and pathways resulting in the breakdown of glycine. GO:0004047 Catalysis of the reaction: N(6)-[(R)-S(8)-aminomethyldihydrolipoyl]-L-lysyl-[protein] + (6S)-5,6,7,8-tetrahydrofolate = N(6)-[(R)-dihydrolipoyl]-L-lysyl-[protein] + (6R)-5,10-methylene-5,6,7,8-tetrahydrofolate + NH4+. GO:0005515 Binding to a protein.

Target profile

Computed evidence for target prioritization.

Human off-target: hit
Human identity (%): 39.355
Human E-value: 2.44e-25
Gut microbiome off-target: hit
Essential (DEG): N
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 0.879

Structure –

Pocket –

Sequence

Primary amino-acid sequence viewer.

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

3 GO

Gene Ontology (GO)

GO:0006546 The chemical reactions and pathways resulting in the breakdown of glycine.
GO:0004047 Catalysis of the reaction: N(6)-[(R)-S(8)-aminomethyldihydrolipoyl]-L-lysyl-[protein] + (6S)-5,6,7,8-tetrahydrofolate = N(6)-[(R)-dihydrolipoyl]-L-lysyl-[protein] + (6R)-5,10-methylene-5,6,7,8-tetrahydrofolate + NH4+.
GO:0005515 Binding to a protein.

Sequence Features

Domain/signature hits from InterPro and related databases.

22 records

Show feature table

Start	End	DB	Term	Name
277	360	FunFam	G3DSA:2.40.30.110:FF:000001	Aminomethyltransferase
231	275	FunFam	G3DSA:4.10.1250.10:FF:000001	Aminomethyltransferase
231	274	Gene3D	G3DSA:4.10.1250.10	Aminomethyltransferase fragment
7	253	Pfam	PF01571	Aminomethyltransferase folate-binding domain
7	253	InterPro	IPR006222	Aminomethyltransferase, folate-binding domain
5	230	Gene3D	G3DSA:3.30.1360.120	Probable tRNA modification gtpase trme; domain 1
5	230	InterPro	IPR027266	GTP-binding protein TrmE/Aminomethyltransferase GcvT, domain 1
51	137	FunFam	G3DSA:3.30.70.1400:FF:000001	Aminomethyltransferase
277	360	Gene3D	G3DSA:2.40.30.110	-
4	356	PANTHER	PTHR43757	AMINOMETHYLTRANSFERASE
4	356	InterPro	IPR028896	Aminomethyltransferase-like
51	137	Gene3D	G3DSA:3.30.70.1400	-
280	353	Pfam	PF08669	Glycine cleavage T-protein C-terminal barrel domain
280	353	InterPro	IPR013977	Glycine cleavage T-protein, C-terminal barrel domain
1	355	Hamap	MF_00259	Aminomethyltransferase [gcvT].
1	355	InterPro	IPR022903	Glycine cleavage system T protein, bacteria
4	276	SUPERFAMILY	SSF103025	Folate-binding domain
4	354	NCBIfam	TIGR00528	glycine cleavage system aminomethyltransferase GcvT
4	354	InterPro	IPR006223	Glycine cleavage system T protein
269	357	SUPERFAMILY	SSF101790	Aminomethyltransferase beta-barrel domain
269	357	InterPro	IPR029043	Glycine cleavage T-protein/YgfZ, C-terminal
1	358	PIRSF	PIRSF006487	GCST

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...

Legend High Medium Low

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
ColabFold PA5215	ColabFold	—	—	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				0.879

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.

55 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
C2F	3A8I	P27248	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…`
FFO	1WOP	Q9WY54	473.4 Da LogP -0.73 TPSA 219.8	1 viol.	✓ Clean	`c1cc(ccc1C(=O)NC(CCC(=O)O)C(=O)O)NCC2CNC3=C(N2C…`
FOA	2GAG	Q3ZDQ8	112.1 Da LogP 0.98 TPSA 50.4	✓ Ro5	✓ Clean	`c1cc(oc1)C(=O)O`
RED	1WOR	Q9WY54	208.3 Da LogP 2.25 TPSA 37.3	✓ Ro5	✓ Clean	`C(CCC(=O)O)C[C@H](CCS)S`
THG	4PAA	Q63342	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
ZINC1529363	1.000	208.3 Da LogP 2.25 TPSA 37.3	✓ Ro5	✓ Clean	`O=C(O)CCCC[C@H](S)CCS`
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@@…`
ZINC3869601	1.000	208.3 Da LogP 2.25 TPSA 37.3	✓ Ro5	✓ Clean	`O=C(O)CCCC[C@@H](S)CCS`
ZINC4228235	1.000	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	1.000	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	1.000	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	1.000	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](…`
ZINC8618631	0.848	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	0.848	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…`
ZINC4228247	0.712	473.4 Da LogP -0.73 TPSA 219.8	1 viol.	✓ Clean	`Nc1nc2c(c(=O)[nH]1)N[C@H](CN(C=O)c1ccc(C(=O)N[C…`
ZINC2005305	0.708	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	0.708	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	0.708	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…`
ZINC9212425	0.689	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	0.689	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	0.689	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	0.689	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…`
ZINC85394426	0.667	206.2 Da LogP 1.80 TPSA 80.6	✓ Ro5	✓ Clean	`O=C(O)c1ccc(C(=O)c2ccco2)o1`
ZINC8618632	0.635	459.5 Da LogP 0.52 TPSA 211.8	1 viol.	✓ Clean	`Nc1nc(O)c2c(n1)NC[C@@H](CCNc1ccc(C(=O)N[C@H](CC…`
ZINC8627115	0.635	459.5 Da LogP 0.52 TPSA 211.8	1 viol.	✓ Clean	`Nc1nc(O)c2c(n1)NC[C@H](CCNc1ccc(C(=O)N[C@H](CCC…`
ZINC4228265	0.630	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…`
ZINC4517559	0.630	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(…`
ZINC12374887	0.630	216.2 Da LogP 2.21 TPSA 67.5	✓ Ro5	✓ Clean	`O=C(O)c1ccc(C(=O)c2ccco2)cc1`
ZINC8655682	0.628	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…`
ZINC13887836	0.616	429.4 Da LogP 0.54 TPSA 187.5	1 viol.	✓ Clean	`Nc1nc2c(c(=O)[nH]1)[C@@H](CCc1ccc(C(=O)N[C@@H](…`
ZINC1710770	0.615	200.2 Da LogP 2.35 TPSA 47.3	✓ Ro5	Alert	`O=C(C(=O)c1ccco1)c1ccccc1`
ZINC4658141	0.608	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](C…`
ZINC4658144	0.608	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](…`
ZINC1613560	0.607	216.2 Da LogP 2.21 TPSA 67.5	✓ Ro5	✓ Clean	`O=C(O)c1ccccc1C(=O)c1ccco1`
ZINC4228269	0.605	456.4 Da LogP -0.61 TPSA 193.7	1 viol.	✓ Clean	`Nc1nc2c(c(=O)[nH]1)[N+]1=CN(c3ccc(C(=O)N[C@@H](…`
ZINC4228270	0.605	456.4 Da LogP -0.61 TPSA 193.7	1 viol.	✓ Clean	`Nc1nc2c(c(=O)[nH]1)[N+]1=CN(c3ccc(C(=O)N[C@@H](…`
ZINC100477623	0.600	204.2 Da LogP 2.33 TPSA 60.4	✓ Ro5	✓ Clean	`O=C(CC(=O)c1ccco1)c1ccco1`
ZINC6472822	0.600	218.2 Da LogP 2.72 TPSA 60.4	✓ Ro5	✓ Clean	`O=C(CCC(=O)c1ccco1)c1ccco1`
ZINC156403	0.593	274.3 Da LogP 1.47 TPSA 66.9	✓ Ro5	✓ Clean	`O=C(c1ccco1)N1CCN(C(=O)c2ccco2)CC1`
ZINC4654270	0.592	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	0.592	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](…`
ZINC13515262	0.589	439.4 Da LogP 1.17 TPSA 187.5	1 viol.	✓ Clean	`Nc1nc2ccc(CNc3ccc(C(=O)N[C@@H](CCC(=O)O)C(=O)O)…`
ZINC4228243	0.584	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	0.584	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	0.584	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(…`
ZINC8664075	0.580	330.3 Da LogP 0.76 TPSA 145.2	1 viol.	✓ Clean	`Nc1nc2c(c(=O)[nH]1)N[C@@H](CCNc1ccc(C(=O)O)cc1)…`
ZINC983943	0.577	360.3 Da LogP 4.16 TPSA 90.6	✓ Ro5	✓ Clean	`O=C(c1cc(C(=O)c2ccco2)cc(C(=O)c2ccco2)c1)c1ccco1`
ZINC77301924	0.573	443.4 Da LogP 0.07 TPSA 204.6	1 viol.	✓ Clean	`Nc1nc2c(c(=O)[nH]1)[C@H](CCc1ccc(C(=O)N[C@H](CC…`
ZINC106891773	0.571	204.2 Da LogP 2.65 TPSA 63.6	✓ Ro5	✓ Clean	`O=C(/C=C(\O)c1ccco1)c1ccco1`
ZINC1567048	0.568	440.4 Da LogP 0.56 TPSA 200.4	1 viol.	✓ Clean	`Nc1nc2ccc(CNc3ccc(C(=O)N[C@@H](CCC(=O)O)C(=O)O)…`
ZINC1995991	0.568	439.4 Da LogP 1.17 TPSA 187.5	1 viol.	✓ Clean	`Nc1nc2ccc(NCc3ccc(C(=O)N[C@@H](CCC(=O)O)C(=O)O)…`
ZINC200768381	0.568	344.3 Da LogP -0.08 TPSA 153.4	✓ Ro5	✓ Clean	`Nc1nc(=O)c2c([nH]1)NC[C@@H](CNc1ccc(C(=O)O)cc1)…`
ZINC200768411	0.568	344.3 Da LogP -0.08 TPSA 153.4	✓ Ro5	✓ Clean	`Nc1nc(=O)c2c([nH]1)NC[C@H](CNc1ccc(C(=O)O)cc1)N…`
ZINC49815930	0.567	216.2 Da LogP 2.21 TPSA 67.5	✓ Ro5	✓ Clean	`O=C(O)c1cccc(C(=O)c2ccco2)c1`
ZINC1560405340	0.561	472.4 Da LogP -0.16 TPSA 220.1	1 viol.	✓ Clean	`Nc1nc(O)c2c(n1)NC[C@H](CNc1ccc(C(=O)N[C](CCC(=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.