KpKP13 Protein target profile

Met repressor

Accession: KP13_00571

Gene: AHE47046.1 metJ 3D evidence: AlphaFold DB model + ColabFold model UniProt A0A0H3GGZ2
Length 105
Pocket druggability (P2Rank · AlphaFold DB model) 0.035
Direct ligand evidence 0 72 total records
Functional annotation 0 EC 7 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
No hit
Gut microbiome similarity
3.1% of screened genomes Lower prevalence suggests narrower overlap with the screened gut microbiome.

Essentiality

Essential (DEG)
Y
DEG identity (%)
96.19 Higher values support similarity to known essential genes.
DEG E-value
5.9199999999999996e-74 Smaller values mean stronger essential-gene similarity.

Structure confidence

ColabFold pLDDT
95.11 0-100 confidence; >70 supports local structural interpretation.

Binding-site evidence

AlphaFold DB / UniProt model

P2Rank's binding-site probability is the primary druggability signal shown across the app; FPocket's druggability score is shown alongside it for comparison. Both estimate small-molecule pocket quality after applying the curated structure priority — neither is experimental binding evidence. The 3D viewer may show a different loaded structure, so visible pockets can differ.

Druggability (P2Rank) 0.035
Structure A0A0H3GGZ2
Pocket Pocket 1
Druggability (FPocket) 0.264
Structure A0A0H3GGZ2
Pocket Pocket 7
ColabFold model
P2Rank 0.027 · Pocket 1
FPocket 0.366 · Pocket 5
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 147 / 4744 genomes with a hit
Prevalence 3.1%

Cross-references

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

Sequence

Primary amino-acid sequence viewer.

MAEWSGEYISPYAEHGKKSEQVKKITVSIPLKVLKILTDERTRRQVNNLRHATNSELLCEAFLHAFTGQPLPNDEDLRKERSDEIPEAAKAIMRELGIDPDTWEY

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

7 GO

Subcellular localization

Localization
Cytoplasmic

Gene Ontology (GO)

7
  • GO:0006555 The chemical reactions and pathways involving L-methionine (2-amino-4-(methylthio)butanoic acid), a sulfur-containing, essential amino acid found in peptide linkage in proteins.
  • GO:0006355 Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
  • GO:0003700 A transcription regulator activity that modulates transcription of gene sets via selective and non-covalent binding to a specific double-stranded genomic DNA sequence (sometimes referred to as a motif) within a cis-regulatory region. Regulatory regions include promoters (proximal and distal) and enhancers. Genes are transcriptional units, and include bacterial operons.
  • GO:0005737 The contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
  • GO:0003677 Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
  • 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.
  • GO:0045892 Any process that stops, prevents, or reduces the frequency, rate or extent of cellular DNA-templated transcription.

Sequence domains and features

Domain and signature matches imported from InterPro and related databases.

11 records
Show feature table
Start End DB Term Name
3 99 Pfam PF01340 Met Apo-repressor, MetJ
3 99 InterPro IPR002084 Methionine repressor MetJ
2 105 FunFam G3DSA:1.10.140.10:FF:000001 Met repressor
2 104 CDD cd00490 Met_repressor_MetJ
2 104 InterPro IPR002084 Methionine repressor MetJ
2 105 SUPERFAMILY SSF47598 Ribbon-helix-helix
2 105 InterPro IPR010985 Ribbon-helix-helix
2 105 Gene3D G3DSA:1.10.140.10 -
2 105 InterPro IPR023453 Methionine repressor MetJ domain superfamily
1 105 Hamap MF_00744 Met repressor [metJ].
1 105 InterPro IPR002084 Methionine repressor MetJ

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 · P2Rank

Druggability (P2Rank): high ≥ 0.5 · medium 0.2–0.49 · low < 0.2

Pocket 1 P2Rank #1
0.035
Show in viewer
Surrounding area

Binding pockets · FPocket

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

Pocket 1 FPocket #7
0.264
Show in viewer
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_A0A0H3GGZ2
AlphaFold DB full sequence Viewing
ColabFold KP13_00571
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.

72 records
Chemistry signal

Bioactivity evidence is available for this target.

Direct evidence 0 same-protein records
Transferred evidence 22 records from similar proteins
Structural ligands 0 0 loaded crystals
Measured bioactivity 22 direct and transferred ChEMBL records
Proposed compounds 50 similarity-based ZINC candidates
Best available ligand signal
CHEMBL1088977 ChEMBL via homolog pchembl 8.40 (~4.0 nM) 398.4 Da · LogP -3.26 · TPSA 185.5 Open detail ChEMBL
CHEMBL1939716 ChEMBL via homolog · pchembl 8.00 (~10.0 nM) Detail ChEMBL
CHEMBL1939715 ChEMBL via homolog · pchembl 7.82 (~15.1 nM) Detail ChEMBL
CHEMBL1939714 ChEMBL via homolog · pchembl 7.44 (~36.3 nM) Detail ChEMBL
CHEMBL1939711 ChEMBL via homolog · pchembl 7.43 (~37.2 nM) Detail ChEMBL

Bioactivity inferred from similar proteins in ChEMBL. Score = pchembl (−log Ki/IC₅₀; higher = more potent).

Show only:
Ligand UniProt (homolog) pchembl MW · LogP · TPSA Lipinski PAINS SMILES
CHEMBL1088977 ChEMBL C3SIU2 8.40 ~4.0 nM 398.4 Da LogP -3.26 TPSA 185.5 1 viol. ✓ Clean C[S+](CC[C@H](N)C(=O)[O-])C[C@H]1O[C@@H](n2cnc3…
CHEMBL1939716 ChEMBL C3SIU2 8.00 ~10.0 nM 1260.9 Da LogP -8.77 TPSA 386.2 3 viol. ✓ Clean C[N+](C)(CC[C@H](N)C(=O)NCc1cccc(CNC(=O)[C@@H](…
CHEMBL1939715 ChEMBL C3SIU2 7.82 ~15.1 nM 1260.9 Da LogP -8.77 TPSA 386.2 3 viol. ✓ Clean C[N+](C)(CC[C@H](N)C(=O)NCc1ccc(CNC(=O)[C@@H](N…
CHEMBL1939714 ChEMBL C3SIU2 7.44 ~36.3 nM 612.5 Da LogP -3.86 TPSA 174.4 1 viol. ✓ Clean C[N+](C)(CC[C@H](N)C(=O)NCc1ccccc1)C[C@H]1O[C@@…
CHEMBL1939711 ChEMBL C3SIU2 7.43 ~37.2 nM 863.0 Da LogP -3.70 TPSA 355.3 3 viol. ✓ Clean CN(CC[C@H](N)C(=O)NCc1cccc(CNC(=O)[C@@H](N)CCN(…
CHEMBL1939710 ChEMBL C3SIU2 7.41 ~38.9 nM 939.1 Da LogP -2.03 TPSA 355.3 3 viol. ✓ Clean CN(CC[C@H](N)C(=O)NCc1ccccc1-c1ccccc1CNC(=O)[C@…
CHEMBL1939726 ChEMBL C3SIU2 7.38 ~41.7 nM 1262.0 Da LogP -6.73 TPSA 336.8 3 viol. ✓ Clean C[N+](C)(CCCC(=O)NCCCCn1nnc2c1CCCCCC2OCCNC(=O)C…
CHEMBL1939723 ChEMBL C3SIU2 7.33 ~46.8 nM 812.9 Da LogP -1.71 TPSA 303.3 3 viol. ✓ Clean CN(CCCC(=O)NCCCCCCNC(=O)CCCN(C)C[C@H]1O[C@@H](n…
CHEMBL1939725 ChEMBL C3SIU2 7.30 ~50.1 nM 1234.0 Da LogP -7.51 TPSA 336.8 3 viol. ✓ Clean C[N+](C)(CCCC(=O)NCCOC1CCCCCc2c1nnn2CCNC(=O)CCC…
CHEMBL1939728 ChEMBL C3SIU2 7.29 ~51.3 nM 1096.8 Da LogP -7.42 TPSA 296.8 3 viol. ✓ Clean C[N+](C)(CCCC(=O)NCCCCCCNC(=O)CCC[N+](C)(C)C[C@…
CHEMBL1939712 ChEMBL C3SIU2 7.21 ~61.7 nM 863.0 Da LogP -3.70 TPSA 355.3 3 viol. ✓ Clean CN(CC[C@H](N)C(=O)NCc1ccc(CNC(=O)[C@@H](N)CCN(C…
CHEMBL1939709 ChEMBL C3SIU2 7.12 ~75.9 nM 939.1 Da LogP -2.03 TPSA 355.3 3 viol. ✓ Clean CN(CC[C@H](N)C(=O)NCc1cccc(-c2cccc(CNC(=O)[C@@H…
CHEMBL1939719 ChEMBL C3SIU2 7.12 ~75.9 nM 978.1 Da LogP -1.03 TPSA 343.2 3 viol. ✓ Clean CN(CCCC(=O)NCCCCn1nnc2c1CCCCCC2OCCNC(=O)CCCN(C)…
CHEMBL1939727 ChEMBL C3SIU2 6.97 ~107.2 nM 1054.7 Da LogP -8.59 TPSA 296.8 3 viol. ✓ Clean C[N+](C)(CCCC(=O)NCCCNC(=O)CCC[N+](C)(C)C[C@H]1…
CHEMBL1939708 ChEMBL C3SIU2 6.96 ~109.6 nM 834.9 Da LogP -5.39 TPSA 355.3 3 viol. ✓ Clean CN(CC[C@H](N)C(=O)NCC#CC#CCNC(=O)[C@@H](N)CCN(C…
CHEMBL1939718 ChEMBL C3SIU2 6.96 ~109.6 nM 950.1 Da LogP -1.81 TPSA 343.2 3 viol. ✓ Clean CN(CCCC(=O)NCCOC1CCCCCc2c1nnn2CCNC(=O)CCCN(C)C[…
CHEMBL1939713 ChEMBL C3SIU2 6.92 ~120.2 nM 470.5 Da LogP -1.01 TPSA 177.7 1 viol. ✓ Clean CN(CC[C@H](N)C(=O)NCc1ccccc1)C[C@H]1O[C@@H](n2c…
CHEMBL1939724 ChEMBL C3SIU2 6.82 ~151.4 nM 549.4 Da LogP -3.59 TPSA 148.4 1 viol. ✓ Clean CCCNC(=O)CCC[N+](C)(C)C[C@H]1O[C@@H](n2cnc3c(N)…
CHEMBL1939722 ChEMBL C3SIU2 6.66 ~218.8 nM 784.9 Da LogP -2.49 TPSA 303.3 3 viol. ✓ Clean CN(CCCC(=O)NCCCCNC(=O)CCCN(C)C[C@H]1O[C@@H](n2c…
CHEMBL1939721 ChEMBL C3SIU2 6.50 ~316.2 nM 770.9 Da LogP -2.88 TPSA 303.3 3 viol. ✓ Clean CN(CCCC(=O)NCCCNC(=O)CCCN(C)C[C@H]1O[C@@H](n2cn…
CHEMBL1939720 ChEMBL C3SIU2 6.16 ~691.8 nM 756.8 Da LogP -3.27 TPSA 303.3 3 viol. ✓ Clean CN(CCCC(=O)NCCNC(=O)CCCN(C)C[C@H]1O[C@@H](n2cnc…
CHEMBL1939717 ChEMBL C3SIU2 6.00 ~1.0 µM 407.5 Da LogP -0.73 TPSA 151.7 ✓ Ro5 ✓ Clean CCCNC(=O)CCCN(C)C[C@H]1O[C@@H](n2cnc3c(N)ncnc32…

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.