KpKP13 Protein target profile

UDP-N-acetylmuramate:L-alanyl-gamma-D-glutamyl- meso-diaminopimelate ligase

Accession: KP13_01257

Gene: mpl AHE46680.1 3D evidence: AlphaFold DB model + ColabFold model UniProt A0A0H3GI91
Length 457
Pocket druggability (P2Rank · AlphaFold DB model) 0.991
Direct ligand evidence 0 56 total records
Functional annotation 1 EC 9 GO
Target summary

Strong target candidate with converging metabolic, structural and chemical evidence.

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
5.8% of screened genomes Lower prevalence suggests narrower overlap with the screened gut microbiome.

Essentiality

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

Structure confidence

ColabFold pLDDT
94.7 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) 0.991
Structure A0A0H3GI91
Pocket Pocket 1
Druggability (FPocket) 0.893
Structure A0A0H3GI91
Pocket Pocket 1
ColabFold model
P2Rank 0.988 · Pocket 1
FPocket 0.762 · Pocket 3
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 275 / 4744 genomes with a hit
Prevalence 5.8%

Sequence

Primary amino-acid sequence viewer.

MRIHILGICGTFMGGLAMLARSLGHEVTGSDANVYPPMSTLLENQGIDLIQGYDPSQLEPRPDLVIIGNAMTRGNPCVEAVLENNIPYMSGPQWLHDFVLRDRWVLAVAGTHGKTTTAGMATWILEACGYKPGFVIGGVPGNFDVSARLGDSPFFVIEADEYDCAFFDKRSKFVHYCPRTLILNNLEFDHADIFDDLKAIQKQFHHLVRIVPGKGKIILPENDINLKQVMAMGCWSEQELVGEQGHWQAKKLNADASQWEVLLDGEKVGEVKWALVGEHNMHNGLMAIAAARHVGVLPADAANALGSFINARRRLELRGEANGVTVYDDFAHHPTAILATLQALRGKVGGTARILAVLEPRSNTMKMGVCKDDLAPSLGRADEVFLLQPQHIPWQVAEVAEACVQPAHWSADVDTLAEMVVKTAHPGDHILVMSNGGFGGIHQKLLDKLAQKAAAAE

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 9 GO

Subcellular localization

Localization
Cytoplasmic

Enzyme Commission (EC)

1

Gene Ontology (GO)

9
  • GO:0009058 A cellular process consisting of the biochemical pathways by which a living organism synthesizes chemical substances. This typically represents the energy-requiring part of metabolism in which simpler substances are transformed into more complex ones.
  • GO:0016881 Catalysis of the ligation of an acid to an amino acid via a carbon-nitrogen bond, with the concomitant hydrolysis of the diphosphate bond in ATP or a similar triphosphate.
  • 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:0005524 Binding to ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
  • 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:0106418 Catalysis of the reaction: ATP + UDP-N-acetyl-alpha-D-muramate + L-alanyl-gamma-D-glutamyl-meso-2,6-diaminoheptanedioate = ADP + phosphate + UDP-N-acetylmuramoyl-L-alanyl-gamma-D-glutamyl-meso-2,6-diaminoheptanedioate.
  • 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: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.
  • 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.

29 records
Show feature table
Start End DB Term Name
17 24 Phobius SIGNAL_PEPTIDE_C_REGION C-terminal region of a signal peptide.
91 313 Gene3D G3DSA:3.40.1190.10 -
91 313 InterPro IPR036565 Mur-like, catalytic domain superfamily
5 16 Phobius SIGNAL_PEPTIDE_H_REGION Hydrophobic region of a signal peptide.
1 90 SUPERFAMILY SSF51984 MurCD N-terminal domain
1 450 Hamap MF_02020 UDP-N-acetylmuramate--L-alanyl-gamma-D-glutamyl-meso-2,6-diaminoheptandioate ligase [mpl].
1 450 InterPro IPR005757 Murein peptide ligase
314 451 FunFam G3DSA:3.90.190.20:FF:000002 UDP-N-acetylmuramate--L-alanyl-gamma-D-glutamyl-meso-2,6-diaminoheptandioate ligase
314 451 Gene3D G3DSA:3.90.190.20 -
314 451 InterPro IPR036615 Mur ligase, C-terminal domain superfamily
91 313 FunFam G3DSA:3.40.1190.10:FF:000003 UDP-N-acetylmuramate--L-alanyl-gamma-D-glutamyl-meso-2,6-diaminoheptandioate ligase
2 101 Pfam PF01225 Mur ligase family, catalytic domain
2 101 InterPro IPR000713 Mur ligase, N-terminal catalytic domain
25 457 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
312 448 SUPERFAMILY SSF53244 MurD-like peptide ligases, peptide-binding domain
312 448 InterPro IPR036615 Mur ligase, C-terminal domain superfamily
1 24 Phobius SIGNAL_PEPTIDE Signal peptide region
95 308 SUPERFAMILY SSF53623 MurD-like peptide ligases, catalytic domain
95 308 InterPro IPR036565 Mur-like, catalytic domain superfamily
1 24 SignalP_EUK SignalP-noTM SignalP-noTM
312 360 Pfam PF02875 Mur ligase family, glutamate ligase domain
312 360 InterPro IPR004101 Mur ligase, C-terminal
1 90 Gene3D G3DSA:3.40.50.720 -
108 291 Pfam PF08245 Mur ligase middle domain
108 291 InterPro IPR013221 Mur ligase, central
1 4 Phobius SIGNAL_PEPTIDE_N_REGION N-terminal region of a signal peptide.
2 453 PANTHER PTHR43445 UDP-N-ACETYLMURAMATE--L-ALANINE LIGASE-RELATED
2 449 NCBIfam TIGR01081 UDP-N-acetylmuramate:L-alanyl-gamma-D-glutamyl-meso-diaminopimelate ligase
2 449 InterPro IPR005757 Murein peptide ligase

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
0.991
Likely same site as FPocket 1 0.5 Å 36 shared residues 100% of smaller site
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Surrounding area
Pocket 2 P2Rank #2
0.037
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Surrounding area
Pocket 3 P2Rank #3
0.027
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Surrounding area
Pocket 4 P2Rank #4
0.018
Likely same site as FPocket 20 4.8 Å 4 shared residues 100% of smaller site
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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 #1
0.893 Unusual size
Likely same site as P2Rank 1 0.5 Å 36 shared residues 100% of smaller site
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Surrounding area
Pocket 2 FPocket #20
0.525
Likely same site as P2Rank 4 4.8 Å 4 shared residues 100% of smaller site
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Surrounding area
Pocket 3 FPocket #11
0.338 Unusual size
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Surrounding area
Residue sets
UniProt: Binding site:110-116
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_A0A0H3GI91
AlphaFold DB full sequence Viewing
ColabFold KP13_01257
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
ANP PDB via homolog 506.2 Da · LogP -2.06 · TPSA 281.9 Open detail RCSB PDB
EPU PDB via homolog Detail RCSB PDB
UD1 PDB via homolog Detail RCSB PDB
UMA PDB via homolog Detail RCSB PDB
UXP 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
ANP RCSB PDB B7GV74 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)…
EPU RCSB PDB P45066 677.4 Da LogP -4.03 TPSA 332.2 3 viol. ✓ Clean CC(=O)N[C@@H]1[C@H]([C@@H]([C@H](O[C@@H]1O[P@@]…
UD1 RCSB PDB P65473 607.4 Da LogP -4.65 TPSA 305.9 3 viol. ✓ Clean CC(=O)N[C@@H]1[C@H]([C@@H]([C@H](O[C@@H]1O[P@@]…
UMA RCSB PDB P45066 750.5 Da LogP -4.65 TPSA 361.3 3 viol. ✓ Clean C[C@@H](C(=O)O)NC(=O)[C@@H](C)O[C@@H]1[C@H]([C@…
UXP RCSB PDB Q9HW02 354.4 Da LogP 2.05 TPSA 118.6 ✓ Ro5 ✓ Clean c1c([nH]nc1Nc2c3c[nH]nc3nc(n2)N4CCCC[C@@H]4CO)C…
UYD RCSB PDB Q9HW02 406.5 Da LogP 3.27 TPSA 116.6 ✓ Ro5 ✓ Clean CC(C)(C)c1cc(nn1C)Nc2c3cn[nH]c3nc(n2)N[C@@H](CO…

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.