Protein profile

KP13_01114

D-alanyl-D-alanine carboxypeptidase dacB bifunctional protein

Genome: KpKP13

Gene: AHE42492.1 dacB Structure source: AlphaFold + ColabFold UniProt A0A0H3H3J2
Amino acids 477
Annotations 2
Features 29
PDB binders 16
Druggability 0.337

Overview

Basic information about this protein and its source genome.

Accession
KP13_01114
Gene
AHE42492.1 dacB
Status
annotated
Amino acids
477
Structure source
AlphaFold + ColabFold

Target profile

Computed evidence for target prioritization.

Human off-target
No hit
Human identity (%)
0.0
Gut microbiome off-target
hit
Essential (DEG)
Y
DEG identity (%)
45.395
DEG E-value
2.0100000000000002e-145
Localization
Periplasmic
ColabFold pLDDT
95.49

Selected Druggability evidence

AlphaFold / UniProt model

Selected Druggability is the FPocket score chosen for ranking using the curated structure priority. The 3D viewer may show a different loaded structure, so its visible pockets can differ.

FPocket 0.337
Structure A0A0H3H3J2
Pocket Pocket 11
P2Rank 0.389
Structure A0A0H3H3J2
Pocket Pocket 1
ColabFold model
FPocket 0.434 · Pocket 10
P2Rank 0.281 · Pocket 1
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 110 / 4744 genomes with a hit
Normalized 0.023

Sequence

Primary amino-acid sequence viewer.

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

2 GO

Gene Ontology (GO)

2
  • GO:0006508 The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.
  • GO:0004185 Catalysis of the hydrolysis of a single C-terminal amino acid residue from the C-terminus of a polypeptide chain by a catalytic mechanism that involves a catalytic triad consisting of a serine nucleophile that is activated by a proton relay involving an acidic residue (e.g. aspartate or glutamate) and a basic residue (usually histidine).

Sequence Features

Domain/signature hits from InterPro and related databases.

29 records
Show feature table
Start End DB Term Name
23 473 SUPERFAMILY SSF56601 beta-lactamase/transpeptidase-like
23 473 InterPro IPR012338 Beta-lactamase/transpeptidase-like
1 5 Phobius SIGNAL_PEPTIDE_N_REGION N-terminal region of a signal peptide.
1 20 Phobius SIGNAL_PEPTIDE Signal peptide region
20 468 Pfam PF02113 D-Ala-D-Ala carboxypeptidase 3 (S13) family
20 468 InterPro IPR000667 Peptidase S13, D-Ala-D-Ala carboxypeptidase C
1 20 SignalP_GRAM_NEGATIVE SignalP-noTM SignalP-noTM
244 477 Gene3D G3DSA:3.40.710.10 -
244 477 InterPro IPR012338 Beta-lactamase/transpeptidase-like
20 85 Gene3D G3DSA:3.40.710.10 -
20 85 InterPro IPR012338 Beta-lactamase/transpeptidase-like
360 374 PRINTS PR00922 D-Ala-D-Ala carboxypeptidase 3 (S13) family signature
360 374 InterPro IPR000667 Peptidase S13, D-Ala-D-Ala carboxypeptidase C
424 437 PRINTS PR00922 D-Ala-D-Ala carboxypeptidase 3 (S13) family signature
424 437 InterPro IPR000667 Peptidase S13, D-Ala-D-Ala carboxypeptidase C
58 77 PRINTS PR00922 D-Ala-D-Ala carboxypeptidase 3 (S13) family signature
58 77 InterPro IPR000667 Peptidase S13, D-Ala-D-Ala carboxypeptidase C
345 359 PRINTS PR00922 D-Ala-D-Ala carboxypeptidase 3 (S13) family signature
345 359 InterPro IPR000667 Peptidase S13, D-Ala-D-Ala carboxypeptidase C
286 308 PRINTS PR00922 D-Ala-D-Ala carboxypeptidase 3 (S13) family signature
286 308 InterPro IPR000667 Peptidase S13, D-Ala-D-Ala carboxypeptidase C
86 176 Gene3D G3DSA:3.50.80.20 -
6 16 Phobius SIGNAL_PEPTIDE_H_REGION Hydrophobic region of a signal peptide.
17 20 Phobius SIGNAL_PEPTIDE_C_REGION C-terminal region of a signal peptide.
20 475 PANTHER PTHR30023 D-ALANYL-D-ALANINE CARBOXYPEPTIDASE
20 475 InterPro IPR000667 Peptidase S13, D-Ala-D-Ala carboxypeptidase C
21 477 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
47 447 NCBIfam TIGR00666 D-alanyl-D-alanine carboxypeptidase/D-alanyl-D-alanine-endopeptidase
47 447 InterPro IPR000667 Peptidase S13, D-Ala-D-Ala carboxypeptidase C

3D Structure

Selected loaded structure. Experimental PDB entries may cover only a portion of the sequence; predicted models typically cover the full protein.

3D visualization script Full viewer

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Structural evidence

0 + 2

Experimental PDB entries and predicted models. Click Switch to display a different structure in the viewer.

Entry Method Resolution Chain Coverage Links Status
AlphaFold AF_A0A0H3H3J2
AlphaFold full sequence Viewing
ColabFold KP13_01114
ColabFold full sequence Loaded
Pocket details FPocket · P2Rank — toggle visibility and zoom from here, or open full viewer

Pockets (FPOCKET)

Showing top-ranked FPocket candidates by druggability. Druggability is color-coded: high (0.7 or higher), medium (0.4 to 0.69), low (below 0.4).

FPOCKET Sticks Spheres Surfaces Druggability Labels Zoom Positions
11 0.337

Pockets (P2RANK)

Showing top-ranked P2Rank candidates by probability. Probability is color-coded per P2Rank calibration: high (≥ 0.5), medium (0.2 – 0.49), low (< 0.2).

P2RANK Sticks Spheres Surfaces Score Probability Labels Zoom Positions
1 5.12 0.235
2 1.88 0.037

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.

72 records

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
33D P39045 102.2 Da LogP 1.41 TPSA 20.2 ✓ Ro5 ✓ Clean CC(C)(C)CCO
AIX P45161 351.4 Da LogP 0.26 TPSA 121.5 ✓ Ro5 ✓ Clean CC1([C@@H](N[C@H](S1)[C@@H](C=O)NC(=O)[C@@H](c2…
B07 P39045 239.0 Da LogP -0.55 TPSA 88.0 ✓ Ro5 ✓ Clean B(CNC(=O)c1c(cccc1OC)OC)(O)O
BH6 P39045 213.4 Da LogP 0.08 TPSA 69.6 ✓ Ro5 ✓ Clean B(CNC(=O)c1ccccc1Cl)(O)O
BIY P39045 217.2 Da LogP 0.48 TPSA 86.6 ✓ Ro5 ✓ Clean CC1([C@@H](NC=C(S1)C(=O)O)C(=O)O)C
BO8 P39045 263.1 Da LogP -2.08 TPSA 153.1 1 viol. ✓ Clean [B-]([C@@H](C)NC(=O)CCCC[C@H](C(=O)O)N)(O)(O)O
CMV P45161 491.6 Da LogP -0.50 TPSA 148.1 ✓ Ro5 ✓ Clean CCN1CCN(C(=O)C1=O)N[C@H](c2ccccc2)C(=O)N[C@H](C…
EWA P39045 253.1 Da LogP -0.17 TPSA 88.0 ✓ Ro5 ✓ Clean B([C@@H](C)NC(=O)c1c(cccc1OC)OC)(O)O
EWB P39045 300.1 Da LogP 0.85 TPSA 89.8 ✓ Ro5 ✓ Clean [B-]([C@@H](C)NC(=O)c1ccccc1Cc2ccccc2)(O)(O)O
FMZ P45161 435.5 Da LogP -0.16 TPSA 139.9 ✓ Ro5 ✓ Clean CC1([C@@H](N[C@H](S1)[C@@H](C=O)NC(=O)[C@@H](c2…
FP5 P39045 193.0 Da LogP -0.64 TPSA 69.6 ✓ Ro5 ✓ Clean B(CNC(=O)Cc1ccccc1)(O)O
HQZ P39045 184.0 Da LogP -2.62 TPSA 106.9 ✓ Ro5 ✓ Clean [B-]([C@@H](C)NS(=O)(=O)C)(O)(O)O
NCF P39045 342.4 Da LogP 0.85 TPSA 116.1 ✓ Ro5 ✓ Clean c1cc(sc1)CC(=O)N[C@@H]([C@@H]2N=C(CCS2)C(=O)O)C…
REC P39045 387.4 Da LogP -0.32 TPSA 179.4 ✓ Ro5 ✓ Clean C=C1CS[C@@H](N=C1C(=O)O)[C@@H](C(=O)O)NC(=O)CCC…
REZ P39844 246.3 Da LogP -0.45 TPSA 129.7 ✓ Ro5 ✓ Clean C[C@H](C(=O)O)NC(=O)CCCC[C@H](C(=O)O)N
TFR P39045 300.3 Da LogP 0.39 TPSA 112.7 ✓ Ro5 ✓ Clean C[C@H]([C@@H](C(F)(F)F)O)NC(=O)CCCC[C@H](C(=O)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.