Protein target profile

KP13_03382

Methylthioribose-1-phosphate isomerase

Genome: KpKP13 Gene: mtnA AHE45761.1 3D evidence: AlphaFold DB model + ColabFold model UniProt A0A0H3GPS7
Length 342
Pocket druggability 0.86
Direct ligand evidence 0 55 total records
Functional annotation 1 EC 4 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 (%)
41.16 Lower values reduce human off-target concern.
Human E-value
8.36e-71
Gut microbiome similarity
1.6% of screened genomes Lower prevalence suggests narrower overlap with the screened gut microbiome.

Essentiality

Essential (DEG)
Y
DEG identity (%)
48.308 Higher values support similarity to known essential genes.
DEG E-value
4.32e-83 Smaller values mean stronger essential-gene similarity.

Localization

Localization
Cytoplasmic

Structure confidence

ColabFold pLDDT
96.02 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 0.86
Structure A0A0H3GPS7
Pocket Pocket 1
P2Rank 0.851
Structure A0A0H3GPS7
Pocket Pocket 1
ColabFold model
FPocket 0.495 · Pocket 7
P2Rank 0.851 · Pocket 1
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 76 / 4744 genomes with a hit
Prevalence 1.6%

Cross-references

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

Sequence

Primary amino-acid sequence viewer.

MQTLQTTSLRVSENQLFILDQQALPQEKRWLAADNVALLVDHIHTLRVRGAPLIGLSASLLLALLAQRGLNRDALQQALETLRAARPTAVNLMNNLDRMKQALAREDYPQALEAEALRLVEEDKQLCDRIAEAGSALVKPGSRLLTHCNTGGLATAGVGTALGVIALAHRQGKVTNVWVDETRPLLQGGRLTAWELGELGVPYQLIADSMAASLMAQGQVDAVWVGADRIAANGDVANKIGTYSLAVLAHYHQIPFYVAAPQTTLDRHCPNGAAIPIEQRAAAEVTGVAGSFGAVQWAPTGAAVYNPAFDVTPAGLISGWVLDSGVVTPAQVAAGAFAPDNG

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 4 GO

Enzyme Commission (EC)

1

Gene Ontology (GO)

4
  • GO:0044249 OBSOLETE. The chemical reactions and pathways resulting in the formation of substances, carried out by individual cells.
  • GO:0044237 OBSOLETE. The chemical reactions and pathways by which individual cells transform chemical substances.
  • GO:0046523 Catalysis of the reaction: S-methyl-5-thio-alpha-D-ribose 1-phosphate = S-methyl-5-thio-D-ribulose 1-phosphate.
  • GO:0019509 OBSOLETE. The generation of L-methionine (2-amino-4-(methylthio)butanoic acid) from methylthioadenosine.

Sequence domains and features

Domain and signature matches imported from InterPro and related databases.

16 records
Show feature table
Start End DB Term Name
6 337 PANTHER PTHR43475 METHYLTHIORIBOSE-1-PHOSPHATE ISOMERASE
8 328 NCBIfam TIGR00512 S-methyl-5-thioribose-1-phosphate isomerase
8 328 InterPro IPR005251 Methylthioribose-1-phosphate isomerase
6 336 Hamap MF_01678 Putative methylthioribose-1-phosphate isomerase [mtnA].
6 336 InterPro IPR005251 Methylthioribose-1-phosphate isomerase
1 174 Gene3D G3DSA:1.20.120.420 -
1 174 InterPro IPR027363 Methylthioribose-1-phosphate isomerase, N-terminal
175 335 Gene3D G3DSA:3.40.50.10470 -
175 335 InterPro IPR042529 Initiation factor 2B-like, C-terminal
140 336 FunFam G3DSA:3.40.50.10470:FF:000006 Methylthioribose-1-phosphate isomerase
8 332 SUPERFAMILY SSF100950 NagB/RpiA/CoA transferase-like
8 332 InterPro IPR037171 NagB/RpiA transferase-like
39 329 NCBIfam TIGR00524 S-methyl-5-thioribose-1-phosphate isomerase
39 329 InterPro IPR011559 Initiation factor 2B alpha/beta/delta
48 329 Pfam PF01008 Initiation factor 2 subunit family
48 329 InterPro IPR000649 Initiation factor 2B-related

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.

Download VMD script Full viewer

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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
0.86
Likely same site as P2Rank 1 0.5 Å 21 shared residues 100% of smaller site
Unusual size
Show in viewer
Surrounding area
Site 2 FPocket #11
0.431
Likely same site as P2Rank 2 3.5 Å 8 shared residues 100% of smaller site
Unusual size
Show in viewer
Surrounding area
Site 3 FPocket #8
0.401
Likely same site as P2Rank 2 7.3 Å 3 shared residues 38% 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
0.851
Likely same site as FPocket 1 0.5 Å 21 shared residues 100% of smaller site
Show in viewer
Surrounding area
Site 2 P2Rank #2
0.031
Likely same site as FPocket 11 3.5 Å 8 shared residues 100% of smaller site
Show in viewer
Surrounding area
Site 3 P2Rank #3
0.011
Show in viewer
Surrounding area
Residue sets
UniProt: Active site:228-228 Proton donor
UniProt: Binding site:187-187
UniProt: Binding site:238-239
UniProt: Binding site:49-51
UniProt: Binding site:86-86
UniProt: Site:148-148 Transition state stabilizer
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_A0A0H3GPS7
AlphaFold DB full sequence Viewing
ColabFold KP13_03382
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
C7B PDB via homolog 451.4 Da · LogP 3.99 · TPSA 76.7 Open detail RCSB PDB
M6P PDB via homolog Detail RCSB PDB
MRU PDB via homolog Detail RCSB PDB
RI2 PDB via homolog Detail RCSB PDB
RUB 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
C7B RCSB PDB P49770 451.4 Da LogP 3.99 TPSA 76.7 ✓ Ro5 ✓ Clean c1cc(ccc1OCC(=O)NC2CCC(CC2)NC(=O)COc3ccc(cc3)Cl…
M6P RCSB PDB Q14232 260.1 Da LogP -3.10 TPSA 156.9 1 viol. ✓ Clean C([C@@H]1[C@H]([C@@H]([C@@H]([C@H](O1)O)O)O)O)O…
MRU RCSB PDB O31662 260.2 Da LogP -1.25 TPSA 124.3 ✓ Ro5 ✓ Clean CSC[C@H]([C@H](C(=O)COP(=O)(O)O)O)O
RI2 RCSB PDB O57947 310.1 Da LogP -2.35 TPSA 183.2 1 viol. ✓ Clean C([C@@H]1[C@H]([C@H]([C@H](O1)OP(=O)(O)O)O)O)OP…
RUB RCSB PDB O57947 310.1 Da LogP -2.50 TPSA 191.0 1 viol. ✓ Clean C([C@H]([C@H](C(=O)COP(=O)(O)O)O)O)OP(=O)(O)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.