Protein target profile

KP13_00697

Penicillin-binding protein 1A

Genome: KpKP13 Gene: mrcA AHE42316.1 3D evidence: AlphaFold DB model + ColabFold model UniProt A0A0H3GZF1
Length 852
Pocket druggability 0.568
Direct ligand evidence 0 68 total records
Functional annotation 2 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
3.0% of screened genomes Lower prevalence suggests narrower overlap with the screened gut microbiome.

Essentiality

Essential (DEG)
Y
DEG identity (%)
42.208 Higher values support similarity to known essential genes.
DEG E-value
9.44e-151 Smaller values mean stronger essential-gene similarity.

Localization

Localization
CytoplasmicMembrane

Structure confidence

ColabFold pLDDT
89.95 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 0.568
Structure A0A0H3GZF1
Pocket Pocket 5
P2Rank 0.566
Structure A0A0H3GZF1
Pocket Pocket 1
ColabFold model
FPocket 0.574 · Pocket 42
P2Rank 0.526 · Pocket 1
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 140 / 4744 genomes with a hit
Prevalence 3.0%

Cross-references

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

Sequence

Primary amino-acid sequence viewer.

MKFVKYLLILAVCCVLLGAGSIFGLYKYIEPQLPDVATLKDVRLQIPMQVYSADGELIAQYGEKRRIPVTLQQIPPELVKAFIATEDSRFYEHHGVDPVGIFRAASVAMFSGHASQGASTITQQLARNFFLSPEKTLMRKIKEAFLAIRIEQLLNKDEILELYLNKIYLGYRAYGVGAAAQVYFGKPIDQLTLSEMAVIAGLPKAPSTFNPLYSMDRATARRNVVLSRMLSEGYITQAQYDEARSEPIDASYHAPKIAFSAPYLSEMVRQEMVNRYGEQAYEDGYRVYTTITRKNQQAAQQAVRNNVLDYDMRHGYRGPASVLWKVGETPWETKKIVDSLKRQSGYGPLFPAVVTSANAQEAVALLANGDSVSLTMEGVRWARRFISDTQQGATPRKVNDVVQAGQQIWVRKVGDSWWLSQLPDVNSALVSINPQNGAIIALVGGFDFNQSKFNRATQALRQVGSNIKPFLYTAAMDKGLTLASMLNDVPISRWDAGAGSDWRPKNSPPQYAGPIRLRQGLGQSKNVVMVRAMRAMGVDYAAEYLQRFGFPAQNIVHTESLALGSASFTPLQVARGYSVMANGGFLVNPFFISKIENDQGGVLFEERPKIACPQCDLPVIYGDTPKSNVLENKDVEDVATSAEPQNGNVPPQPQLEQANQSLVAQSGAQEYAPHVINTPLAFLIKSALNSNIFGEPGWMGTGWRAGRDLQRHDIGGKTGTTNSSKDAWFSGYGPGVVTSVWIGFDDHRRDLGRTTASGAIKDQISGYEGGAKSAQPAWDSFMKSVLEGVPEEPLTPPPGIVTVNIDRSTGQLANGGNSRAEYFIEGTQPTQQAVREVGTTLTDGGGETHELF

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

2 EC 10 GO

Enzyme Commission (EC)

2

Gene Ontology (GO)

10
  • GO:0008658 Binding to penicillin, an antibiotic that contains the condensed beta-lactamthiazolidine ring system.
  • GO:0030288 The region between the inner (cytoplasmic or plasma) membrane and outer membrane of organisms with two membranes such as Gram negative bacteria. These periplasmic spaces are relatively thick and contain a thin peptidoglycan layer (PGL), also referred to as a thin cell wall.
  • 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:0008955 Catalysis of the reaction: [GlcNAc-(1->4)-Mur2Ac(oyl-L-Ala-gamma-D-Glu-L-Lys-D-Ala-D-Ala)](n)-di-trans,octa-cis-undecaprenyl diphosphate + beta-D-GlcNAc-(1->4)-Mur2Ac(oyl-L-Ala-gamma-D-Glu-L-Lys-D-Ala-D-Ala)-di-trans,octa-cis-undecaprenyl diphosphate = [GlcNAc-(1->4)-Mur2Ac(oyl-L-Ala-gamma-D-Glu-L-Lys-D-Ala-D-Ala)](n+1)-di-trans-octa-cis-undecaprenyl diphosphate + di-trans,octa-cis-undecaprenyl diphosphate + H+.
  • GO:0009002 Catalysis of the reaction: (Ac)2-L-Lys-D-alanyl-D-alanine + H2O = (Ac)2-L-Lys-D-alanine + D-alanine.
  • 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:0006508 The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.
  • GO:0008360 Any process that modulates the surface configuration of a cell.
  • GO:0046677 Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an antibiotic stimulus. An antibiotic is a chemical substance produced by a microorganism which has the capacity to inhibit the growth of or to kill other microorganisms.

Sequence domains and features

Domain and signature matches imported from InterPro and related databases.

27 records
Show feature table
Start End DB Term Name
55 229 Pfam PF00912 Transglycosylase
55 229 InterPro IPR001264 Glycosyl transferase, family 51
25 852 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
243 326 Gene3D G3DSA:3.40.710.10 -
243 326 InterPro IPR012338 Beta-lactamase/transpeptidase-like
48 242 Gene3D G3DSA:1.10.3810.10 -
48 242 InterPro IPR036950 Penicillin binding protein transglycosylase domain
243 332 FunFam G3DSA:3.40.710.10:FF:000013 Penicillin-binding protein 1A
43 257 SUPERFAMILY SSF53955 Lysozyme-like
43 257 InterPro IPR023346 Lysozyme-like domain superfamily
397 834 FunFam G3DSA:3.40.710.10:FF:000010 Penicillin-binding protein 1A
65 786 NCBIfam TIGR02074 PBP1A family penicillin-binding protein
2 837 PANTHER PTHR32282 BINDING PROTEIN TRANSPEPTIDASE, PUTATIVE-RELATED
1 6 Phobius SIGNAL_PEPTIDE_N_REGION N-terminal region of a signal peptide.
7 29 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
395 834 Gene3D G3DSA:3.40.710.10 -
395 834 InterPro IPR012338 Beta-lactamase/transpeptidase-like
429 603 Pfam PF00905 Penicillin binding protein transpeptidase domain
429 603 InterPro IPR001460 Penicillin-binding protein, transpeptidase
1 24 Phobius SIGNAL_PEPTIDE Signal peptide region
18 24 Phobius SIGNAL_PEPTIDE_C_REGION C-terminal region of a signal peptide.
211 832 SUPERFAMILY SSF56601 beta-lactamase/transpeptidase-like
211 832 InterPro IPR012338 Beta-lactamase/transpeptidase-like
7 17 Phobius SIGNAL_PEPTIDE_H_REGION Hydrophobic region of a signal peptide.
48 242 FunFam G3DSA:1.10.3810.10:FF:000003 Penicillin-binding protein 1a
316 425 Pfam PF17092 Penicillin-binding protein OB-like domain
316 425 InterPro IPR031376 Penicillin-binding protein, OB-like domain

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 #5
0.568
Show in viewer
Surrounding area

Binding pockets · P2Rank

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

Site 1 P2Rank #1
0.566
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Surrounding area
Site 2 P2Rank #2
0.311
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Surrounding area
Site 3 P2Rank #3
0.08
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Surrounding area
Site 4 P2Rank #4
0.062
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Surrounding area
Site 5 P2Rank #5
0.011
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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_A0A0H3GZF1
AlphaFold DB full sequence Viewing
ColabFold KP13_00697
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.

68 records
Chemistry signal

Structural and bioactivity evidence are both available for this target.

Direct evidence 0 same-protein records
Transferred evidence 18 records from similar proteins
Structural ligands 11 0 loaded crystals
Measured bioactivity 7 direct and transferred ChEMBL records
Proposed compounds 50 similarity-based ZINC candidates
Best available ligand signal
2U4 PDB via homolog 664.6 Da · LogP -1.00 · TPSA 318.0 Open detail RCSB PDB
AZR PDB via homolog Detail RCSB PDB
BMG PDB via homolog Detail RCSB PDB
CB9 PDB via homolog Detail RCSB PDB
DXF 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
2U4 RCSB PDB Q07806 664.6 Da LogP -1.00 TPSA 318.0 3 viol. Alert CC(C)(C(=O)O)O/N=C(/c1csc(n1)N)\C(=O)N[C@@H](CO…
AZR RCSB PDB G1C794 437.5 Da LogP -1.23 TPSA 210.4 ✓ Ro5 ✓ Clean C[C@@H]([C@@H](C=O)NC(=O)/C(=N\OC(C)(C)C(=O)O)/…
BMG RCSB PDB Q04707 352.4 Da LogP -1.95 TPSA 111.2 ✓ Ro5 ✓ Clean C[C@@H]1[C@@H](NC(=C1S[C@@H]2Cn3cnc[n+]3C2)C(=O…
CB9 RCSB PDB Q8Y547 380.4 Da LogP 0.43 TPSA 132.8 ✓ Ro5 ✓ Clean CC1([C@@H](N[C@H](S1)[C@@H](C=O)NC(=O)[C@H](c2c…
DXF RCSB PDB Q8Y547 426.4 Da LogP -0.59 TPSA 182.6 ✓ Ro5 ✓ Clean CO/N=C(/c1ccco1)\C(=O)N[C@H](C=O)[C@@H]2NC(=C(C…
IM2 RCSB PDB G1C794 301.4 Da LogP -0.23 TPSA 122.5 ✓ Ro5 ✓ Clean [H]/N=C/NCCSC1=C(N[C@H](C1)[C@H](C=O)[C@@H](C)O…
M0E RCSB PDB Q9R744 1580.6 Da LogP -2.25 TPSA 607.7 3 viol. ✓ Clean C[C@@H]1[C@H]([C@@H]([C@H]([C@@H](O1)O[C@@H]2[C…
PNM RCSB PDB G1C794 336.4 Da LogP 0.81 TPSA 95.5 ✓ Ro5 ✓ Clean CC1([C@@H](N[C@H](S1)[C@@H](C=O)NC(=O)Cc2ccccc2…
TEB RCSB PDB Q04707 385.5 Da LogP 0.61 TPSA 102.2 ✓ Ro5 ✓ Clean C[C@@H]1[C@@H](NC(=C1SC2CN(C2)C3=NCCS3)C(=O)O)[…
TLA RCSB PDB Q8Y547 150.1 Da LogP -2.12 TPSA 115.1 ✓ Ro5 ✓ Clean [C@@H]([C@H](C(=O)O)O)(C(=O)O)O
UE1 RCSB PDB G1C794 715.7 Da LogP -5.06 TPSA 355.7 3 viol. ✓ Clean CC(C)(C(=O)[O-])O/N=C(/c1csc(n1)N)\C(=O)N[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.