Protein target profile

VK055_2353

D-methionine ABC transporter, ATP-binding protein

Genome: KpATCC43816 Gene: metN AIK80950.1 3D evidence: AlphaFold DB model + ColabFold model UniProt A0A0H3GS83
Length 343
Pocket druggability 0.434
Direct ligand evidence 0 56 total records
Functional annotation 0 EC 6 GO
Target summary

Target candidate with partial support; inspect missing evidence before prioritizing.

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 (%)
67.647 Lower values reduce human off-target concern.
Human E-value
1.01e-07
Gut microbiome similarity
9.1% of screened genomes Lower prevalence suggests narrower overlap with the screened gut microbiome.

Essentiality

Essential (DEG)
Y
DEG identity (%)
46.154 Higher values support similarity to known essential genes.
DEG E-value
6.31e-11 Smaller values mean stronger essential-gene similarity.

Localization

Localization
CytoplasmicMembrane

Structure confidence

ColabFold pLDDT
91.29 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 0.434
Structure A0A0H3GS83
Pocket Pocket 6
P2Rank 0.247
Structure A0A0H3GS83
Pocket Pocket 1
ColabFold model
FPocket 0.386 · Pocket 5
P2Rank 0.269 · Pocket 1
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 433 / 4744 genomes with a hit
Prevalence 9.1%

Cross-references

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

Sequence

Primary amino-acid sequence viewer.

MIKLSNITKVFQQGNRSIQALNNVSLHVPAGQIYGVIGASGAGKSTLIRCVNLLERPTEGSVQVDGQELTALSEKELTRARRQIGMIFQHFNLLASRTVFGNVALPLELDNTPQAEIKRRVTELLDLVGLGDKHDSYPANLSGGQKQRVAIARALASNPKVLLCDEATSALDPATTRSILELLKDINRRLGLTILLITHEMDVVKRICDCVAVISNGQLIEQDTVSEVFSHPKTPLAQQFIQSTLHLDIPDDYQARLKPTATADSVPMLRMEFTGHSVDAPLLSETARRFNVNNNIISAQMDYAGGVKFGIMLTEMHGTQEDTQAAIAWLQEHHVKVEVLGYV

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

6 GO

Gene Ontology (GO)

6
  • GO:0005524 Binding to ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
  • GO:0048473 The process in which D-methionine is transported across a lipid bilayer, from one side of a membrane to the other.
  • GO:0033232 Enables the transfer of a solute or solutes from one side of a membrane to the other according to the reaction: ATP + H2O + D-methionine(out/in) = ADP + phosphate + D-methionine(in/out).
  • GO:0009276 The peptidoglycan layer of the Gram-negative cell envelope. In Gram-negative cells the peptidoglycan is relatively thin (1-2nm) and is linked to the outer membrane by lipoproteins. In Gram-negative cells the peptidoglycan is too thin to retain the primary stain in the Gram staining procedure and therefore cells appear red after Gram stain.
  • GO:0016887 Catalysis of the reaction: ATP + H2O = ADP + H+ phosphate. ATP hydrolysis is used in some reactions as an energy source, for example to catalyze a reaction or drive transport against a concentration gradient.
  • GO:0005886 The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.

Sequence domains and features

Domain and signature matches imported from InterPro and related databases.

26 records
Show feature table
Start End DB Term Name
248 343 SUPERFAMILY SSF55021 ACT-like
248 343 InterPro IPR045865 ACT-like domain
2 242 PANTHER PTHR43166 AMINO ACID IMPORT ATP-BINDING PROTEIN
1 240 SUPERFAMILY SSF52540 P-loop containing nucleoside triphosphate hydrolases
1 240 InterPro IPR027417 P-loop containing nucleoside triphosphate hydrolase
1 233 CDD cd03258 ABC_MetN_methionine_transporter
1 233 InterPro IPR041701 Methionine import ATP-binding protein MetN, ATP-binding domain
246 343 Gene3D G3DSA:3.30.70.260 -
265 340 SMART SM00930 NIL_2
265 340 InterPro IPR018449 NIL domain
1 232 FunFam G3DSA:3.40.50.300:FF:000233 Methionine import ATP-binding protein MetN
2 241 ProSiteProfiles PS50893 ATP-binding cassette, ABC transporter-type domain profile.
2 241 InterPro IPR003439 ABC transporter-like, ATP-binding domain
268 339 Pfam PF09383 NIL domain
268 339 InterPro IPR018449 NIL domain
30 217 SMART SM00382 AAA_5
30 217 InterPro IPR003593 AAA+ ATPase domain
141 155 ProSitePatterns PS00211 ABC transporters family signature.
141 155 InterPro IPR017871 ABC transporter-like, conserved site
246 343 FunFam G3DSA:3.30.70.260:FF:000014 Methionine import ATP-binding protein MetN
1 232 Gene3D G3DSA:3.40.50.300 -
1 232 InterPro IPR027417 P-loop containing nucleoside triphosphate hydrolase
21 169 Pfam PF00005 ABC transporter
21 169 InterPro IPR003439 ABC transporter-like, ATP-binding domain
1 343 NCBIfam TIGR02314 methionine ABC transporter ATP-binding protein MetN
1 343 InterPro IPR012692 ABC transporter, methionine import, ATP-binding protein MetN, proteobacteria

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 #6
0.434
Likely same site as P2Rank 4 1.0 Å 11 shared residues 100% of smaller site
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Surrounding area
Site 2 FPocket #2
0.2
Likely same site as P2Rank 3 1.9 Å 8 shared residues 100% of smaller site
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Surrounding area

Binding pockets · P2Rank

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

Site 1 P2Rank #1
0.247
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Surrounding area
Site 2 P2Rank #2
0.133
Show in viewer
Surrounding area
Site 3 P2Rank #3
0.075
Likely same site as FPocket 2 1.9 Å 8 shared residues 100% of smaller site
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Surrounding area
Site 4 P2Rank #4
0.042
Likely same site as FPocket 6 1.0 Å 11 shared residues 100% of smaller site
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Surrounding area
Site 5 P2Rank #5
0.004
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Surrounding area
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_A0A0H3GS83
AlphaFold DB full sequence Viewing
ColabFold VK055_2353
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.

56 records
Chemistry signal

Structural ligand evidence is available for this target.

Direct evidence 0 same-protein records
Transferred evidence 6 records from similar proteins
Structural ligands 6 0 loaded crystals
Measured bioactivity 0 direct and transferred ChEMBL records
Proposed compounds 50 similarity-based ZINC candidates
Best available ligand signal
2BA PDB via homolog 658.4 Da · LogP -1.63 · TPSA 309.7 Open detail RCSB PDB
AGS PDB via homolog Detail RCSB PDB
ANP PDB via homolog Detail RCSB PDB
AT4 PDB via homolog Detail RCSB PDB
BET 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
2BA RCSB PDB Q9KIF7 658.4 Da LogP -1.63 TPSA 309.7 3 viol. ✓ Clean c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@H]4[C@H](O3)C…
AGS RCSB PDB P30750 523.2 Da LogP -1.51 TPSA 262.1 3 viol. ✓ Clean c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)…
ANP RCSB PDB D0VWX4 506.2 Da LogP -2.06 TPSA 281.9 3 viol. ✓ Clean c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)…
AT4 RCSB PDB A0A0D8G707 443.3 Da LogP -0.81 TPSA 212.4 2 viol. ✓ Clean c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)…
BET RCSB PDB Q9KIF7 118.2 Da LogP -0.22 TPSA 37.3 ✓ Ro5 ✓ Clean C[N+](C)(C)CC(=O)O
LPP RCSB PDB Q9HVW1 648.9 Da LogP 10.51 TPSA 119.4 2 viol. ✓ Clean CCCCCCCCCCCCCCCC(=O)OC[C@H](COP(=O)(O)O)OC(=O)C…

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.