KpKP13 Protein target profile

N-acetylmuramoyl-L-alanine amidase amiD

Accession: KP13_04238

Gene: amiD AHE45469.1 3D evidence: AlphaFold DB model + ColabFold model UniProt A0A0H3GKW4
Length 276
Pocket druggability (P2Rank · AlphaFold DB model) 0.328
Direct ligand evidence 0 48 total records
Functional annotation 1 EC 5 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
No hit
Gut microbiome similarity
1.8% of screened genomes Lower prevalence suggests narrower overlap with the screened gut microbiome.

Essentiality

Essential (DEG)
Y
DEG identity (%)
76.364 Higher values support similarity to known essential genes.
DEG E-value
1.82e-154 Smaller values mean stronger essential-gene similarity.

Structure confidence

ColabFold pLDDT
94.77 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) 0.328
Structure A0A0H3GKW4
Pocket Pocket 1
Druggability (FPocket) 0.401
Structure A0A0H3GKW4
Pocket Pocket 8
ColabFold model
P2Rank 0.411 · Pocket 1
FPocket 0.448 · Pocket 3
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 85 / 4744 genomes with a hit
Prevalence 1.8%

Sequence

Primary amino-acid sequence viewer.

MKRMMRIVLLALLLTGCAGEKGIIDRDGYQLDTRHPAQAAYPRIKVLVIHYTADNFDVSLATLTDKEVSSHYLIPEQPPRYQHKPRIWQLVPEEDLAWHAGVSYWRGSTRINDTSIGIELENRGWQKTAGVKSFTPFHPEQIAALIPLARDIIARYHIAPQNVVAHADIAPQRKDDPGPLFPWQQLAQQGIGAWPDEQRVAFYLNGRPASEPVDPEIVLDLLSRYGYQVTPEMTPAQKKRVIIAFQMHFRPQRWDGVADAQTEAIAEALLEKYGQG

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 5 GO

Subcellular localization

Localization
Unknown

Enzyme Commission (EC)

1

Gene Ontology (GO)

5
  • GO:0009253 The chemical reactions and pathways resulting in the breakdown of peptidoglycans, any of a class of glycoconjugates found in bacterial cell walls and consisting of long glycan strands of alternating residues of beta-(1,4) linked N-acetylglucosamine and N-acetylmuramic acid, cross-linked by short peptides.
  • GO:0008745 Catalysis of the hydrolysis of the link between N-acetylmuramoyl residues and L-amino acid residues in certain bacterial cell-wall glycopeptides.
  • GO:0019867 The external membrane of Gram-negative bacteria or certain organelles such as mitochondria and chloroplasts; freely permeable to most ions and metabolites.
  • GO:0071555 A process that results in the assembly, arrangement of constituent parts, or disassembly of the cell wall, the rigid or semi-rigid envelope lying outside the cell membrane of plant, fungal and most prokaryotic cells, maintaining their shape and protecting them from osmotic lysis.
  • GO:0009254 The continual breakdown and regeneration of peptidoglycan required to maintain the bacterial cell wall. Peptidoglycans consist of long glycan strands of alternating residues of beta-(1,4) linked N-acetylglucosamine and N-acetylmuramic acid, cross-linked by short peptides.

Sequence domains and features

Domain and signature matches imported from InterPro and related databases.

25 records
Show feature table
Start End DB Term Name
7 14 Phobius SIGNAL_PEPTIDE_H_REGION Hydrophobic region of a signal peptide.
1 19 SignalP_EUK SignalP-noTM SignalP-noTM
42 179 Pfam PF01510 N-acetylmuramoyl-L-alanine amidase
42 179 InterPro IPR002502 N-acetylmuramoyl-L-alanine amidase domain
43 180 CDD cd06583 PGRP
43 180 InterPro IPR002502 N-acetylmuramoyl-L-alanine amidase domain
36 269 PANTHER PTHR30417 N-ACETYLMURAMOYL-L-ALANINE AMIDASE AMID
32 178 SMART SM00644 ami_2
32 178 InterPro IPR002502 N-acetylmuramoyl-L-alanine amidase domain
42 192 FunFam G3DSA:3.40.80.10:FF:000003 N-acetylmuramoyl-L-alanine amidase
43 192 Gene3D G3DSA:3.40.80.10 -
43 192 InterPro IPR036505 N-acetylmuramoyl-L-alanine amidase/PGRP domain superfamily
1 20 SignalP_GRAM_NEGATIVE SignalP-noTM SignalP-noTM
1 6 Phobius SIGNAL_PEPTIDE_N_REGION N-terminal region of a signal peptide.
16 42 Gene3D G3DSA:6.20.370.150 -
23 194 SUPERFAMILY SSF55846 N-acetylmuramoyl-L-alanine amidase-like
23 194 InterPro IPR036505 N-acetylmuramoyl-L-alanine amidase/PGRP domain superfamily
198 273 SUPERFAMILY SSF47090 PGBD-like
198 273 InterPro IPR036365 PGBD-like superfamily
1 19 Phobius SIGNAL_PEPTIDE Signal peptide region
20 276 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
193 276 Gene3D G3DSA:1.10.101.10 -
193 276 InterPro IPR036366 PGBD superfamily
15 19 Phobius SIGNAL_PEPTIDE_C_REGION C-terminal region of a signal peptide.
1 17 ProSiteProfiles PS51257 Prokaryotic membrane lipoprotein lipid attachment site profile.

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 · P2Rank

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

Pocket 1 P2Rank #1
0.328
Likely same site as FPocket 1 2.4 Å 12 shared residues 86% of smaller site
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Surrounding area
Pocket 2 P2Rank #2
0.013
Show in viewer
Surrounding area

Binding pockets · FPocket

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

Pocket 1 FPocket #8
0.401
Show in viewer
Surrounding area
Pocket 2 FPocket #1
0.243
Likely same site as P2Rank 1 2.4 Å 12 shared residues 86% of smaller site
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_A0A0H3GKW4
AlphaFold DB full sequence Viewing
ColabFold KP13_04238
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.

48 records
Chemistry signal

Structural ligand evidence is available for this target.

Direct evidence 0 same-protein records
Transferred evidence 2 records from similar proteins
Structural ligands 2 0 loaded crystals
Measured bioactivity 0 direct and transferred ChEMBL records
Proposed compounds 46 similarity-based ZINC candidates
Best available ligand signal
FLC PDB via homolog 189.1 Da · LogP -5.25 · TPSA 140.6 Open detail RCSB PDB
J0J PDB via homolog Detail RCSB PDB
ZINC15722130 ZINC proposed compound · Tanimoto 0.745 Detail ZINC
ZINC255987061 ZINC proposed compound · Tanimoto 0.745 Detail ZINC
ZINC255987062 ZINC proposed compound · Tanimoto 0.745 Detail ZINC

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
FLC RCSB PDB Q9HT86 189.1 Da LogP -5.25 TPSA 140.6 ✓ Ro5 ✓ Clean C(C(=O)[O-])C(CC(=O)[O-])(C(=O)[O-])O
J0J RCSB PDB Q9HT86 461.5 Da LogP -2.66 TPSA 251.2 1 viol. ✓ Clean C[C@H](C(=O)N[C@H](CCC(=O)N[C@@H](CCC[C@H](C(=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.

Cross-references

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