Protein target profile

VK055_5052

DD-carboxypeptidase, penicillin-binding protein 6b

Genome: KpATCC43816 Gene: AIK83578.1 3D evidence: AlphaFold DB model + ColabFold model Metabolism 4 reactions UniProt A0A0H3GV65
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Length 347
Pocket druggability 0.551
Metabolic reactions 4
Chokepoint No
Direct ligand evidence 0 65 total records
Functional annotation 1 EC 8 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.

Main supporting evidence

No similar human protein detected The current BLAST sequence screen did not find a significant human match, lowering apparent off-target risk. Core gene across strains Marked as conserved by both pan-genome tools: Roary and CoreCruncher. Moderate predicted binding pocket FPocket selected-pocket score 0.55. This supports review but is not experimental validation. Structure available AlphaFold DB model + ColabFold model Review the complete evidence below

Risks to review

Microbiome similarity 112 of 4744 screened genomes (2.4%) have a significant similarity hit. This target also has a predicted binding pocket (FPocket 0.55) — check the ligand evidence before deprioritizing on off-target risk alone. Weak second pocket-predictor signal P2Rank predicted binding-site probability 0.28.

Evidence coverage

Core evidence streams are available for this target.
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
2.4% of screened genomes Lower prevalence suggests narrower overlap with the screened gut microbiome.

Essentiality

Essential (DEG)
Y
DEG identity (%)
46.356 Higher values support similarity to known essential genes.
DEG E-value
8.49e-111 Smaller values mean stronger essential-gene similarity.

Localization

Localization
CytoplasmicMembrane

Structure confidence

ColabFold pLDDT
95.23 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 0.551
Structure A0A0H3GV65
Pocket Pocket 13
P2Rank 0.28
Structure A0A0H3GV65
Pocket Pocket 1
ColabFold model
FPocket 0.494 · Pocket 1
P2Rank 0.3 · Pocket 1
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 112 / 4744 genomes with a hit
Prevalence 2.4%

Cross-references

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

Sequence

UniProt A0A0H3GV65

Chemistry

ChEMBL CHEMBL520642

Pathways

BioCyc RXN-16649[CCO-PERI-BAC]-CPD-17927/WATER//CPD-17926/D-ALANINE.51. BioCyc RXN-16659[CCO-PERI-BAC]-A-DONOR-PG-WITH-MESODAP-PENTAPEPTIDE/AN-ACCEPTOR-PG-WITH-MESODAP-TETRAPEPTIDE//CPD0-2718/D-ALANINE.113. BioCyc RXN-16649[CCO-CYTOSOL]-CPD-17927/WATER//CPD-17926/D-ALANINE.50. BioCyc RXN-16659[CCO-CYTOSOL]-A-DONOR-PG-WITH-MESODAP-PENTAPEPTIDE/AN-ACCEPTOR-PG-WITH-MESODAP-TETRAPEPTIDE//CPD0-2718/D-ALANINE.112.

Metabolic context

Reactions catalyzed, pathway membership, and centrality in the genome-scale metabolic network.

Explore metabolic network

Metabolic context: no human homolog detected.

Relative network centrality 0.0% more central than 0.0% of genes in this genome
Chokepoint Not a chokepoint
Pathways

No specific KEGG pathway assigned - this reaction either has no KEGG mapping, or only matches a generic overview map with no route-level information.

Catalyzed reactions

4 reactions mapped to this gene in the metabolic model. Open the full network to see each one, with substrates/products and the reaction-reaction map.

Imported from KpATCC43816.sbml · 2026-07-09

Sequence

Primary amino-acid sequence viewer.

MDYTTGQVLTAGNEHQQRNPASLTKLMTGYVVDRAIDSHRITFDDIVTVGKDAWAKGNPVFDGSSLMFLKPGDRVSVRDLSRGLIVDSGNDACVALADYVAGGQPQFVALMNQYVEKLHLRDTHFETVHGLDAPGQHSSAYDLAVLSRAIIHGEPDVYHMYSQKSLTWNGITQQNRNGLLWDKTMNVDGLKTGHTSGAGFNLIASAVDGQRRLIAVVMGADSPKGREQQAAKLLHWGQQNFDTVQVLQKGQKVGTERIWYGDKEQIKLGTDQDFWLALPKAEVSRIKAKYVLDKKDLEAPIAANQRVGEISLYDGDKVVGHYPLVTLESINKGGVFSRMSDYLHHEL

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 8 GO

Enzyme Commission (EC)

1

Gene Ontology (GO)

8
  • GO:0004180 Catalysis of the hydrolysis of a single C-terminal amino acid residue from a polypeptide chain.
  • GO:0006508 The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.
  • GO:0009002 Catalysis of the reaction: (Ac)2-L-Lys-D-alanyl-D-alanine + H2O = (Ac)2-L-Lys-D-alanine + D-alanine.
  • 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:0008658 Binding to penicillin, an antibiotic that contains the condensed beta-lactamthiazolidine ring system.
  • 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.

21 records
Show feature table
Start End DB Term Name
1 240 Gene3D G3DSA:3.40.710.10 -
1 240 InterPro IPR012338 Beta-lactamase/transpeptidase-like
241 332 Pfam PF07943 Penicillin-binding protein 5, C-terminal domain
241 332 InterPro IPR012907 Peptidase S11, D-Ala-D-Ala carboxypeptidase A, C-terminal
241 331 Gene3D G3DSA:2.60.410.10 -
241 331 InterPro IPR037167 D-Ala-D-Ala carboxypeptidase, C-terminal domain superfamily
241 332 SMART SM00936 PBP5_C_2
241 334 SUPERFAMILY SSF69189 Penicillin-binding protein associated domain
241 334 InterPro IPR015956 Penicillin-binding protein, C-terminal domain superfamily
1 221 Pfam PF00768 D-alanyl-D-alanine carboxypeptidase
1 221 InterPro IPR001967 Peptidase S11, D-alanyl-D-alanine carboxypeptidase A, N-terminal
80 97 PRINTS PR00725 D-Ala-D-Ala carboxypeptidase 1 (S11) family signature
80 97 InterPro IPR018044 Peptidase S11, D-alanyl-D-alanine carboxypeptidase A
107 120 PRINTS PR00725 D-Ala-D-Ala carboxypeptidase 1 (S11) family signature
107 120 InterPro IPR018044 Peptidase S11, D-alanyl-D-alanine carboxypeptidase A
21 32 PRINTS PR00725 D-Ala-D-Ala carboxypeptidase 1 (S11) family signature
21 32 InterPro IPR018044 Peptidase S11, D-alanyl-D-alanine carboxypeptidase A
2 245 PANTHER PTHR21581 D-ALANYL-D-ALANINE CARBOXYPEPTIDASE
1 241 SUPERFAMILY SSF56601 beta-lactamase/transpeptidase-like
1 241 InterPro IPR012338 Beta-lactamase/transpeptidase-like
1 240 FunFam G3DSA:3.40.710.10:FF:000001 D-alanyl-D-alanine serine-type carboxypeptidase

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 #13
0.551
Show in viewer
Surrounding area

Binding pockets · P2Rank

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

Site 1 P2Rank #1
0.28
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Surrounding area
Site 2 P2Rank #2
0.036
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Surrounding area
Site 3 P2Rank #3
0.009
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Surrounding area
Site 4 P2Rank #4
0.001
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Surrounding area
Residue sets
UniProt: Active site:24-24 Acyl-ester intermediate
UniProt: Active site:27-27 Proton acceptor
UniProt: Active site:90-90
UniProt: Binding site:193-193
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_A0A0H3GV65
AlphaFold DB — — full sequence — Viewing
ColabFold VK055_5052
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.

65 records
Chemistry signal

Structural and bioactivity evidence are both available for this target.

Direct evidence 0 same-protein records
Transferred evidence 15 records from similar proteins
Structural ligands 14 0 loaded crystals
Measured bioactivity 1 direct and transferred ChEMBL records
Proposed compounds 50 similarity-based ZINC candidates
Best available ligand signal
AI8 PDB via homolog 607.7 Da · LogP 1.24 · TPSA 185.7 Open detail RCSB PDB
AIC PDB via homolog Detail RCSB PDB
BO9 PDB via homolog Detail RCSB PDB
CEW PDB via homolog Detail RCSB PDB
CXV 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
AI8 RCSB PDB
5TW4
A0A0H2WY27 607.7 Da LogP 1.24 TPSA 185.7 2 viol. ✓ Clean CCON=C(c1nc(sn1)N)C(=O)N[C@H](C=O)[C@@H]2NC(=C(…
AIC RCSB PDB
3ITA
P08506 349.4 Da LogP 0.32 TPSA 112.7 ✓ Ro5 ✓ Clean CC1([C@@H](N2[C@H](S1)[C@@H](C2=O)NC(=O)[C@@H](…
BO9 RCSB PDB
1Z6F
P0AEB2 580.4 Da LogP 0.84 TPSA 212.6 2 viol. ✓ Clean B([C@@H](C)NC(=O)[C@H](CCCCNC(=O)OCc1ccccc1)NC(…
CEW RCSB PDB
3HUM
A0A0H2WY27 401.5 Da LogP -0.89 TPSA 155.1 ✓ Ro5 ✓ Clean CC1=C(N[C@H](SC1)[C@@H](C=O)NC(=O)C(=NOC)C2=CSC…
CXV RCSB PDB
3MZD
P0AEB2 437.9 Da LogP 2.50 TPSA 121.5 ✓ Ro5 ✓ Clean Cc1c(c(no1)c2ccccc2Cl)C(=O)N[C@@H](C=O)[C@@H]3N…
HJ2 RCSB PDB
3BEC
P0AEB2 389.4 Da LogP -0.45 TPSA 179.0 1 viol. ✓ Clean CC1=C(N[C@H](SC1)[C@@H](C(=O)O)NC(=O)CCCC[C@@H]…
HJ3 RCSB PDB
3BEB
P0AEB2 375.4 Da LogP -0.46 TPSA 158.8 ✓ Ro5 ✓ Clean CC1([C@@H](N[C@H](S1)[C@@H](C=O)NC(=O)CCCC[C@@H…
IM2 RCSB PDB
3MZF
P0AEB2 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…
MXR RCSB PDB
6NTZ
P0AEB2 385.5 Da LogP -0.35 TPSA 119.3 ✓ Ro5 ✓ Clean C[C@H]1[C@@H](C(=N[C@H]1[C@H](C=O)[C@@H](C)O)C(…
NFF RCSB PDB
5TY2
A0A0H2WY27 416.5 Da LogP 2.43 TPSA 104.7 ✓ Ro5 ✓ Clean CCOc1ccc2ccccc2c1C(=O)N[C@H](C=O)[C@@H]3N[C@H](…
OK3 RCSB PDB
5J8X
P0AEB2 357.2 Da LogP 0.04 TPSA 142.1 ✓ Ro5 ✓ Clean [B-]1([C@H](Cc2cccc(c2O1)C(=O)O)NC(=O)c3ccc(cc3…
RB6 RCSB PDB
5TX9
A0A0H2WY27 536.6 Da LogP -1.50 TPSA 212.2 3 viol. ✓ Clean C1CNC[C@@H]1N2CC=C(C2=O)CC3=C(N[C@H](SC3)[C@@H]…
SIN RCSB PDB
4K91
A0A0H2ZFH3 118.1 Da LogP -0.06 TPSA 74.6 ✓ Ro5 ✓ Clean C(CC(=O)O)C(=O)O
ZZ7 RCSB PDB
3HUN
A0A0H2WY27 367.4 Da LogP 0.15 TPSA 141.8 ✓ Ro5 ✓ Clean CC1([C@@H](N[C@H](S1)[C@@H](C(=O)O)NC(=O)[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.