Protein target profile

KP13_31803

glycine cleavage system aminomethyltransferase T

Genome: KpKP13 Gene: AHE42746.1 gcvT 3D evidence: AlphaFold DB model + ColabFold model UniProt A0A0H3H2N5
Length 375
Pocket druggability 0.944
Direct ligand evidence 0 55 total records
Functional annotation 0 EC 3 GO
Target summary

Promising target candidate with multiple supporting evidence streams.

Automated synthesis of the evidence currently loaded. Review the underlying records before prioritizing this protein.

Terms and data sources used on this page

PDB: experimentally determined structures from the Protein Data Bank. These are the strongest structural evidence, but may cover only part of the protein.

AlphaFold DB model: a precomputed predicted structure downloaded from AlphaFold Database/UniProt, not an experiment performed here.

ColabFold model: a predicted structure generated for this workspace; interpret it with coverage and confidence.

pLDDT: confidence score for predicted structures. High values support local geometry; low values mean the region should not drive pocket interpretation.

FPocket / P2Rank: software tools that predict possible ligand-binding pockets on a 3D structure. They are useful screening signals, not experimental validation.

Druggability: a pocket-based estimate of whether a small molecule could bind productively. It does not mean a drug already exists.

PDB ligand: a compound observed in an experimental structure. Direct same-protein records are stronger than homolog-transferred records.

ChEMBL: a public database of measured compound bioactivity. Direct entries are stronger than entries transferred from similar proteins.

ZINC: a purchasable-compound database. Here it marks proposed candidates from chemical similarity, not measured binders.

LigQ / LigQ_2: an internal Target pipeline step that gathers PDB, ChEMBL, and ZINC ligand evidence for each protein.

Off-target: sequence similarity to proteins we prefer not to hit, such as human proteins or beneficial gut microbiome proteins.

DEG: Database of Essential Genes. A match suggests the protein resembles genes known to be essential in other organisms.

Roary / CoreCruncher: pan-genome tools used to decide whether a gene is core across analyzed strains or accessory/strain-specific.

EC / GO: functional annotations: EC describes enzyme reactions; GO describes biological process, molecular function, or cellular component.

KEGG pathway: a curated metabolic route label used here to group reactions imported from the metabolic model.

Chokepoint: a metabolic reaction that is the only producer or consumer of a metabolite in the imported model.

Prioritization evidence

Selectivity, essentiality, structural confidence, conservation, and predicted binding-site evidence.

Off-target risk

Human off-target
Hit
Human identity (%)
34.191 Lower values reduce human off-target concern.
Human E-value
1.99e-39
Gut microbiome similarity
3.0% of screened genomes Lower prevalence suggests narrower overlap with the screened gut microbiome.

Essentiality

Essential (DEG)
N
DEG identity (%)
0.0 Higher values support similarity to known essential genes.

Localization

Localization
Cytoplasmic

Structure confidence

ColabFold pLDDT
95.98 0-100 confidence; >70 supports local structural interpretation.

Binding-site evidence

AlphaFold DB / UniProt model

The selected pocket score is the FPocket value used for ranking after applying the curated structure priority. It estimates small-molecule pocket quality; it is not experimental binding evidence. The 3D viewer may show a different loaded structure, so visible pockets can differ.

FPocket 0.944
Structure A0A0H3H2N5
Pocket Pocket 1
P2Rank 0.927
Structure A0A0H3H2N5
Pocket Pocket 1
ColabFold model
FPocket 0.979 · Pocket 12
P2Rank 0.932 · Pocket 1
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 144 / 4744 genomes with a hit
Prevalence 3.0%

Cross-references

External database identifiers for this protein, its structures, ligands, and metabolic reactions.

Sequence

Primary amino-acid sequence viewer.

MAGSVLFDEEKMAQQTPLYEQHTLCGARMVDFHGWMMPLHYGSQIDEHHAVRGDAGMFDVSHMTIVDFHGSRIREFLRYLLANDVAKLTTPGKALYTGMLTASAGVIDDLIVYFLSEDYFRLVVNSATREKDLAWISEQAEPYGLEITVRDDLSLIAVQGPQAKAKAATLFTDAQRQAVEGMKPFFGVQAGDLFIATTGYTGEAGYEIAMPNEQAADFWRGLLDAGVKPCGLGARDTLRLEAGMNLYGQEMDEGVSPLAANMGWTIAWEPADRNFIGREALEMQREKGTEQLVGLVMTEKGVLRGGLPVRFTDSDGNQKEGIITSGTFSPTLGYSIALARVPAGIGDTAVVQIRNREMPVKVTKPGFVRNGKAIV

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

3 GO

Gene Ontology (GO)

3
  • GO:0006546 The chemical reactions and pathways resulting in the breakdown of glycine.
  • GO:0005515 Binding to a protein.
  • 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+.

Sequence domains and features

Domain and signature matches imported from InterPro and related databases.

22 records
Show feature table
Start End DB Term Name
288 375 Gene3D G3DSA:2.40.30.110 -
18 265 Pfam PF01571 Aminomethyltransferase folate-binding domain
18 265 InterPro IPR006222 Aminomethyltransferase, folate-binding domain
282 372 SUPERFAMILY SSF101790 Aminomethyltransferase beta-barrel domain
282 372 InterPro IPR029043 Glycine cleavage T-protein/YgfZ, C-terminal
16 242 Gene3D G3DSA:3.30.1360.120 Probable tRNA modification gtpase trme; domain 1
16 242 InterPro IPR027266 GTP-binding protein TrmE/Aminomethyltransferase GcvT, domain 1
243 287 Gene3D G3DSA:4.10.1250.10 Aminomethyltransferase fragment
4 374 PIRSF PIRSF006487 GCST
243 287 FunFam G3DSA:4.10.1250.10:FF:000001 Aminomethyltransferase
12 370 PANTHER PTHR43757 AMINOMETHYLTRANSFERASE
12 370 InterPro IPR028896 Aminomethyltransferase-like
62 150 FunFam G3DSA:3.30.70.1400:FF:000001 Aminomethyltransferase
288 375 FunFam G3DSA:2.40.30.110:FF:000001 Aminomethyltransferase
13 370 NCBIfam TIGR00528 glycine cleavage system aminomethyltransferase GcvT
13 370 InterPro IPR006223 Glycine cleavage system T protein
12 370 Hamap MF_00259 Aminomethyltransferase [gcvT].
12 370 InterPro IPR022903 Glycine cleavage system T protein, bacteria
14 288 SUPERFAMILY SSF103025 Folate-binding domain
291 367 Pfam PF08669 Glycine cleavage T-protein C-terminal barrel domain
291 367 InterPro IPR013977 Glycine cleavage T-protein, C-terminal barrel domain
62 149 Gene3D G3DSA:3.30.70.1400 -

3D structure

Selected loaded structure. Experimental PDB entries may cover only a portion of the sequence; AlphaFold DB and ColabFold models typically cover the full protein but remain computational predictions.

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Pocket score High Medium Low
How colors and pocket overlays are used
Uniform protein color marks the displayed model as a single molecular object.
Experimental PDB structures may be colored by chain to distinguish subunits or copies present in the file.
Pocket colors and alpha spheres are evidence overlays for predicted binding cavities; they are not alternative protein chains.
'Alpha spheres' is FPocket's own cavity-shape geometry, imported when available and aligned with the loaded structure.
'Pocket atoms'/'Predicted site atoms' show the pocket's residue atoms instead: P2Rank reports residues rather than alpha spheres, and FPocket falls back to this when alpha-sphere geometry is unavailable or doesn't align.
'No pocket geometry' means neither alpha spheres nor residue-position data could be found for that pocket; the layer just highlights the same residues as 'Nearby residues'.
Pocket details Inspect a specific pocket, or open the full viewer

Binding pockets · FPocket

Druggability: high ≥ 0.7 · medium 0.4–0.69 · low < 0.4

Site 1 FPocket #1
0.944
Likely same site as P2Rank 1 2.2 Å 29 shared residues 94% of smaller site
Unusual size
Show in viewer
Surrounding area

Binding pockets · P2Rank

Probability: high ≥ 0.5 · medium 0.2–0.49 · low < 0.2

Site 1 P2Rank #1
0.927
Likely same site as FPocket 1 2.2 Å 29 shared residues 94% of smaller site
Show in viewer
Surrounding area
Site 2 P2Rank #2
0.036
Show in viewer
Surrounding area
Residue sets
UniProt: Binding site:196-196
All structural evidence 0 experimental · 2 predicted

Structural evidence

0 + 2

Experimental PDB entries plus predicted AlphaFold DB or ColabFold models. Click Switch to display a different loaded structure in the viewer.

Entry Method Resolution Chain Coverage Links Status
AlphaFold DB AF_A0A0H3H2N5
AlphaFold DB full sequence Viewing
ColabFold KP13_31803
ColabFold full sequence Loaded

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
Chemistry signal

Structural ligand evidence is available for this target.

Direct evidence 0 same-protein records
Transferred evidence 5 records from similar proteins
Structural ligands 5 0 loaded crystals
Measured bioactivity 0 direct and transferred ChEMBL records
Proposed compounds 50 similarity-based ZINC candidates
Best available ligand signal
C2F PDB via homolog 459.5 Da · LogP -0.26 · TPSA 202.8 Open detail RCSB PDB
FFO PDB via homolog Detail RCSB PDB
FOA PDB via homolog Detail RCSB PDB
RED PDB via homolog Detail RCSB PDB
THG PDB via homolog Detail RCSB PDB

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.

Show only:
Ligand Source crystal UniProt (homolog) MW · LogP · TPSA Lipinski PAINS SMILES
C2F RCSB PDB 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 RCSB PDB 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 RCSB PDB Q3ZDQ8 112.1 Da LogP 0.98 TPSA 50.4 ✓ Ro5 ✓ Clean c1cc(oc1)C(=O)O
RED RCSB PDB Q9WY54 208.3 Da LogP 2.25 TPSA 37.3 ✓ Ro5 ✓ Clean C(CCC(=O)O)C[C@H](CCS)S
THG RCSB PDB 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…

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.