KpKP13 Protein target profile

Phospho-N-acetylmuramoyl-pentapeptide- transferase

Accession: KP13_01908

Gene: mraY AHE46349.1 3D evidence: AlphaFold DB model + ColabFold model UniProt A0A0H3GI63
Length 360
Pocket druggability (P2Rank · AlphaFold DB model) 0.848
Direct ligand evidence 0 37 total records
Functional annotation 1 EC 10 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
6.7% of screened genomes Lower prevalence suggests narrower overlap with the screened gut microbiome.

Essentiality

Essential (DEG)
Y
DEG identity (%)
98.056 Higher values support similarity to known essential genes.
DEG E-value
0.0 Smaller values mean stronger essential-gene similarity.

Structure confidence

ColabFold pLDDT
91.95 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) 0.848
Structure A0A0H3GI63
Pocket Pocket 1
Druggability (FPocket) 0.685
Structure A0A0H3GI63
Pocket Pocket 2
ColabFold model
P2Rank 0.818 · Pocket 1
FPocket 0.857 · Pocket 3
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 320 / 4744 genomes with a hit
Prevalence 6.7%

Sequence

Primary amino-acid sequence viewer.

MLVWLAEHLVKYYSGFNVFSYLTFRAIVSLLTALFISLWMGPRMIARLQKLAFGQVVRNDGPESHFSKRGTPTMGGIMILTAITVSVLLWAYPSNPYVWCVLTVLIGYGIIGFVDDYRKVVRKDTKGLIARWKYFWMSVIALGVAFALYLAGKDTPATELVVPFFKDVMPQLGLFYILLAYFVIVGTGNAVNLTDGLDGLAIMPTVFVAAGFALVAWATGNMNFANYLHIPYLRHAGELVIVCTAIVGAGLGFLWFNTYPAQVFMGDVGSLALGGALGIIAVLLRQEFLLVIMGGVFVVETLSVILQVGSFKLRGQRIFRMAPIHHHYELKGWPEPRVIVRFWIISLMLVLIGLATLKVR

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 10 GO

Subcellular localization

Localization
CytoplasmicMembrane

Enzyme Commission (EC)

1

Gene Ontology (GO)

10
  • GO:0016020 A lipid bilayer along with all the proteins and protein complexes embedded in it and attached to it.
  • GO:0008963 Catalysis of the reaction: di-trans,octa-cis-undecaprenyl phosphate + UDP-N-acetyl-alpha-D-muramoyl-L-alanyl-gamma-D-glutamyl-L-lysyl-D-alanyl-D-alanine = Mur2Ac(oyl-L-Ala-gamma-D-Glu-L-Lys-D-Ala-D-Ala)-di-trans,octa-cis-undecaprenyl diphosphate + UMP.
  • GO:0016780 Catalysis of the transfer of a substituted phosphate group, other than diphosphate or nucleotidyl residues, from one compound (donor) to a another (acceptor).
  • GO:0005886 The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.
  • GO:0046872 Binding to a metal ion.
  • GO:0051992 Catalysis of the reaction: di-trans,octa-cis-undecaprenyl phosphate + UDP-N-acetyl-alpha-D-muramoyl-L-alanyl-gamma-D-glutamyl-meso-2,6-diaminopimeloyl-D-alanyl-D-alanine = di-trans-octa-cis-undecaprenyl diphospho-N-acetyl-alpha-D-muramoyl-L-alanyl-D-glutamyl-meso-2,6-diaminopimeloyl-D-alanyl-D-alanine + UMP.
  • GO:0051301 The process resulting in division and partitioning of components of a cell to form more cells; may or may not be accompanied by the physical separation of a cell into distinct, individually membrane-bounded daughter cells.
  • 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:0009252 The chemical reactions and pathways resulting in the formation 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:0008360 Any process that modulates the surface configuration of a cell.

Sequence domains and features

Domain and signature matches imported from InterPro and related databases.

46 records
Show feature table
Start End DB Term Name
358 360 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
234 256 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
285 289 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
61 356 CDD cd06852 GT_MraY
61 356 InterPro IPR003524 Phospho-N-acetylmuramoyl-pentapeptide transferase
1 19 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
68 80 Pfam PF10555 Phospho-N-acetylmuramoyl-pentapeptide-transferase signature 1
68 80 InterPro IPR018480 Phospho-N-acetylmuramoyl-pentapeptide transferase, conserved site
20 40 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
25 358 Hamap MF_00038 Phospho-N-acetylmuramoyl-pentapeptide-transferase [mraY].
25 358 InterPro IPR003524 Phospho-N-acetylmuramoyl-pentapeptide transferase
200 219 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
68 80 ProSitePatterns PS01347 MraY family signature 1.
338 357 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
115 133 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
20 42 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
99 284 Pfam PF00953 Glycosyl transferase family 4
99 284 InterPro IPR000715 Glycosyl transferase, family 4
41 72 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
263 285 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
194 199 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
134 152 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
200 219 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
134 151 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
257 262 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
220 238 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
97 114 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
37 360 NCBIfam TIGR00445 phospho-N-acetylmuramoyl-pentapeptide-transferase
37 360 InterPro IPR003524 Phospho-N-acetylmuramoyl-pentapeptide transferase
312 337 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
289 311 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
23 358 PANTHER PTHR22926 PHOSPHO-N-ACETYLMURAMOYL-PENTAPEPTIDE-TRANSFERASE
23 358 InterPro IPR000715 Glycosyl transferase, family 4
239 256 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
96 114 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
153 171 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
290 311 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
75 92 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
172 193 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
73 90 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
171 193 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
263 284 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
189 200 ProSitePatterns PS01348 MraY family signature 2.
189 200 InterPro IPR018480 Phospho-N-acetylmuramoyl-pentapeptide transferase, conserved site
91 95 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
338 357 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.

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
0.848
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Surrounding area
Pocket 2 P2Rank #2
0.168
Likely same site as FPocket 2 0.6 Å 13 shared residues 100% of smaller site
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Surrounding area
Pocket 3 P2Rank #3
0.14
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Surrounding area
Pocket 4 P2Rank #4
0.041
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Surrounding area
Pocket 5 P2Rank #5
0.037
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Surrounding area

Binding pockets · FPocket

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

Pocket 1 FPocket #2
0.685
Likely same site as P2Rank 2 0.6 Å 13 shared residues 100% of smaller site
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Surrounding area
Pocket 2 FPocket #5
0.41
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Surrounding area
Pocket 3 FPocket #3
0.363
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Surrounding area
Residue sets
UniProt: Binding site:192-192
UniProt: Binding site:267-267
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_A0A0H3GI63
AlphaFold DB full sequence Viewing
ColabFold KP13_01908
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.

37 records
Chemistry signal

Structural and bioactivity evidence are both available for this target.

Direct evidence 0 same-protein records
Transferred evidence 37 records from similar proteins
Structural ligands 2 0 loaded crystals
Measured bioactivity 35 direct and transferred ChEMBL records
Proposed compounds 0 similarity-based ZINC candidates
Best available ligand signal
NK4 PDB via homolog 798.0 Da · LogP 1.05 · TPSA 250.3 Open detail RCSB PDB
NKD PDB via homolog Detail RCSB PDB
CHEMBL4286766 ChEMBL via homolog · pchembl 10.80 (~0.0 nM) Detail ChEMBL
CHEMBL4284923 ChEMBL via homolog · pchembl 10.03 (~0.1 nM) Detail ChEMBL
CHEMBL4279378 ChEMBL via homolog · pchembl 9.49 (~0.3 nM) Detail ChEMBL

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
NK4 RCSB PDB O66465 798.0 Da LogP 1.05 TPSA 250.3 3 viol. ✓ Clean CCCCCCCCCCCCCCCCC[C@H]1CN([C@H](C(=O)N([C@@H]1C…
NKD RCSB PDB O66465 856.9 Da LogP -1.83 TPSA 328.0 3 viol. ✓ Clean C[C@@H]([C@@H](C(=O)N/C=C\1/[C@H]([C@H]([C@@H](…

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.