Protein profile

PA3047

D-alanyl-D-alanine carboxypeptidase

Genome: NC_002516.2

Gene: PA3047 Structure source: AlphaFold UniProt Q9HZG1
Amino acids 476
Annotations 5
Features 29
PDB binders 16
Druggability 0.762

Overview

Basic information about this protein and its source genome.

Accession
PA3047
Gene
PA3047
Status
annotated
Amino acids
476
Structure source
AlphaFold

Target profile

Computed evidence for target prioritization.

Human off-target
No hit
Gut microbiome off-target
hit
Essential (DEG)
N
Localization
Periplasmic

Selected Druggability evidence

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 0.762
Structure
Pocket

Sequence

Primary amino-acid sequence viewer.

MFKSLRTLAFATLLPFALPTLAQVNATLPANVQKALQTNKLTGNDLSLVLIPLDGPGNPTYYNADVSVNPASTMKLFTTYAALEMLGPTYQWKTEFYTDGQLKNGVLNGNLYLKGGGDPKLNMEKLWLLMRDLRANGVTKVTGDLVLDRSYFNIPQLPVFNDDGGDDTKPFLVGPDSLLVNLKSVRMVVRTDGNKVNVQMDPPLANVRIDNQVKMTAPATCPAWPKLRFSPVTQFDGTTLLATGQIPQGCSAQTYMSLLDHPGYTAGAVRGIWQELGGSILGKDRQGSVPRNATLIAKAFSPDLVEIIRDINKYSNNTMARQLFLSIGAQFRNSADGDDAQAAQRVVRQWLARKGITAPRLVMENGSGLSRQERVSAREMAAMLQAAWHSPYAAEYISSLPLAGLDGTMRKRLRRTALVGEAHVKTGTLNTVRALAGFSRDASGHNWVVVAILNSPRPWGASAILDQVLLSLHARK

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

5 GO

Gene Ontology (GO)

5
  • GO:0004175 Catalysis of the hydrolysis of internal, alpha-peptide bonds in a polypeptide chain.
  • 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).
  • 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:0000270 The chemical reactions and pathways involving peptidoglycans, any of a class of glycoconjugates found only 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.

Sequence Features

Domain/signature hits from InterPro and related databases.

29 records
Show feature table
Start End DB Term Name
1 22 Phobius SIGNAL_PEPTIDE Signal peptide region
96 163 FunFam G3DSA:3.50.80.20:FF:000002 D-alanyl-D-alanine carboxypeptidase dacB
1 22 SignalP_GRAM_POSITIVE SignalP-TM SignalP-TM
1 22 SignalP_EUK SignalP-noTM SignalP-noTM
7 474 PANTHER PTHR30023 D-ALANYL-D-ALANINE CARBOXYPEPTIDASE
7 474 InterPro IPR000667 Peptidase S13, D-Ala-D-Ala carboxypeptidase C
19 22 Phobius SIGNAL_PEPTIDE_C_REGION C-terminal region of a signal peptide.
62 454 NCBIfam TIGR00666 D-alanyl-D-alanine carboxypeptidase/D-alanyl-D-alanine-endopeptidase
62 454 InterPro IPR000667 Peptidase S13, D-Ala-D-Ala carboxypeptidase C
1 6 Phobius SIGNAL_PEPTIDE_N_REGION N-terminal region of a signal peptide.
23 476 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
7 18 Phobius SIGNAL_PEPTIDE_H_REGION Hydrophobic region of a signal peptide.
92 163 Gene3D G3DSA:3.50.80.20 -
27 469 SUPERFAMILY SSF56601 beta-lactamase/transpeptidase-like
27 469 InterPro IPR012338 Beta-lactamase/transpeptidase-like
30 454 Pfam PF02113 D-Ala-D-Ala carboxypeptidase 3 (S13) family
30 454 InterPro IPR000667 Peptidase S13, D-Ala-D-Ala carboxypeptidase C
280 468 Gene3D G3DSA:3.40.710.10 -
280 468 InterPro IPR012338 Beta-lactamase/transpeptidase-like
355 369 PRINTS PR00922 D-Ala-D-Ala carboxypeptidase 3 (S13) family signature
355 369 InterPro IPR000667 Peptidase S13, D-Ala-D-Ala carboxypeptidase C
68 87 PRINTS PR00922 D-Ala-D-Ala carboxypeptidase 3 (S13) family signature
68 87 InterPro IPR000667 Peptidase S13, D-Ala-D-Ala carboxypeptidase C
370 384 PRINTS PR00922 D-Ala-D-Ala carboxypeptidase 3 (S13) family signature
370 384 InterPro IPR000667 Peptidase S13, D-Ala-D-Ala carboxypeptidase C
432 445 PRINTS PR00922 D-Ala-D-Ala carboxypeptidase 3 (S13) family signature
432 445 InterPro IPR000667 Peptidase S13, D-Ala-D-Ala carboxypeptidase C
295 317 PRINTS PR00922 D-Ala-D-Ala carboxypeptidase 3 (S13) family signature
295 317 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 + 1

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

Entry Method Resolution Chain Coverage Links Status
AlphaFold PA3047
AlphaFold full sequence Viewing
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
1 0.762
3 0.568
6 0.24

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.