Protein profile

PA4110

beta-lactamase

Genome: NC_002516.2

Gene: PA4110 ampC Structure source: Experimental + AlphaFold UniProt P24735 UniProt Q541D8
Amino acids 397
Annotations 5
Features 17
PDB binders 22
Druggability 0.719

Overview

Basic information about this protein and its source genome.

Accession
PA4110
Gene
PA4110 ampC
Status
annotated
Amino acids
397
Structure source
Experimental + 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 0.719
Structure
Pocket

Sequence

Primary amino-acid sequence viewer.

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 4 GO

Enzyme Commission (EC)

1

Gene Ontology (GO)

4
  • 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:0008800 Catalysis of the reaction: a beta-lactam + H2O = a substituted beta-amino acid.
  • GO:0017001 The chemical reactions and pathways resulting in the breakdown of antibiotic, a substance produced by or derived from certain fungi, bacteria, and other organisms, that can destroy or inhibit the growth of other microorganisms.
  • 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 Features

Domain/signature hits from InterPro and related databases.

17 records
Show feature table
Start End DB Term Name
1 7 Phobius SIGNAL_PEPTIDE_N_REGION N-terminal region of a signal peptide.
38 384 PANTHER PTHR46825 D-ALANYL-D-ALANINE-CARBOXYPEPTIDASE/ENDOPEPTIDASE AMPH
27 397 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
1 26 SignalP_GRAM_NEGATIVE SignalP-noTM SignalP-noTM
1 26 Phobius SIGNAL_PEPTIDE Signal peptide region
1 26 SignalP_GRAM_POSITIVE SignalP-TM SignalP-TM
20 26 Phobius SIGNAL_PEPTIDE_C_REGION C-terminal region of a signal peptide.
38 385 Pfam PF00144 Beta-lactamase
38 385 InterPro IPR001466 Beta-lactamase-related
86 93 ProSitePatterns PS00336 Beta-lactamase class-C active site.
86 93 InterPro IPR001586 Beta-lactamase, class-C active site
32 387 SUPERFAMILY SSF56601 beta-lactamase/transpeptidase-like
32 387 InterPro IPR012338 Beta-lactamase/transpeptidase-like
8 19 Phobius SIGNAL_PEPTIDE_H_REGION Hydrophobic region of a signal peptide.
29 388 Gene3D G3DSA:3.40.710.10 -
29 388 InterPro IPR012338 Beta-lactamase/transpeptidase-like
29 388 FunFam G3DSA:3.40.710.10:FF:000012 Beta-lactamase

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

22 + 1

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

Entry Method Resolution Chain Coverage Links Status
PDB 4WZ4
X-ray 1.05 Å A
90.7% 29-388
Viewing
PDB 6UQU
X-ray 1.09 Å A
93.5% 27-397
Loaded
PDB 4OOY
X-ray 1.10 Å A
90.4% 29-387
Loaded
PDB 6UQT
X-ray 1.25 Å A
93.5% 27-397
Loaded
PDB 4WYY
X-ray 1.28 Å A
90.7% 29-388
Loaded
PDB 8SDR
X-ray 1.35 Å A
100.0% 1-397
Loaded
PDB 6UQS
X-ray 1.37 Å A
93.5% 27-397
Loaded
PDB 8SDT
X-ray 1.38 Å A
100.0% 1-397
Loaded
PDB 2WZX
X-ray 1.40 Å A
93.5% 27-397
Loaded
PDB 3S1Y
X-ray 1.40 Å A
93.5% 27-397
Loaded
PDB 8SDV
X-ray 1.42 Å A
100.0% 1-397
Loaded
PDB 6UR3
X-ray 1.42 Å A
93.5% 27-397
Loaded
PDB 2WZZ
X-ray 1.57 Å A
93.5% 27-397
Loaded
PDB 8SDS
X-ray 1.63 Å A
100.0% 1-397
Loaded
PDB 3S22
X-ray 1.65 Å A
93.5% 27-397
Loaded
PDB 4X68
X-ray 1.68 Å A,B
89.7% 32-387
Loaded
PDB 8SDL
X-ray 1.75 Å A
100.0% 1-397
Loaded
PDB 6S1S
X-ray 1.78 Å A
100.0% 1-397
Loaded
PDB 4GZB
X-ray 1.79 Å A
93.5% 27-397
Loaded
PDB 4HEF
X-ray 1.86 Å A
90.7% 29-388
Loaded
PDB 4NK3
X-ray 1.90 Å A
93.5% 27-397
Loaded
PDB 8SDN
X-ray 2.10 Å A
100.0% 1-397
Loaded
AlphaFold PA4110
AlphaFold 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
1 0.719
4 0.231

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 16.7 0.785
2 4.42 0.186
3 2.59 0.074
4 1.85 0.036
5 1.27 0.013

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.

172 records

Highest-confidence structural evidence: ligands co-crystallized with this exact protein. If the source PDB is loaded in TPW, use Open crystal to inspect it in the structure viewer.

Show only:
Ligand Source crystal MW · LogP · TPSA Lipinski PAINS SMILES
3S2 322.4 Da LogP -1.27 TPSA 127.8 ✓ Ro5 ✓ Clean CNCCCCNC(=O)N1CC[C@H]([C@H]1C=O)NS(=O)(=O)O
3VT 314.1 Da LogP 1.12 TPSA 101.8 ✓ Ro5 ✓ Clean B1(c2cc(c(c(c2[C@H](O1)CC(=O)O)C)C)Oc3cnccn3)O
3VU 335.2 Da LogP 0.76 TPSA 127.8 ✓ Ro5 ✓ Clean B1(c2cc(c(c(c2[C@H](O1)CC(=O)O)C)C)Oc3nc(ns3)N)O
KRT 192.0 Da LogP -0.54 TPSA 77.8 ✓ Ro5 ✓ Clean B(c1cccc(c1)/C=C/C(=O)O)(O)O
MK7 350.4 Da LogP -1.83 TPSA 137.1 ✓ Ro5 ✓ Clean C1C[C@H](N(C[C@@H]1NOS(=O)(=O)O)C=O)C(=O)NC2CCN…
NXL 267.3 Da LogP -2.21 TPSA 139.0 ✓ Ro5 ✓ Clean C1C[C@H](N(C[C@@H]1NOS(=O)(=O)O)C=O)C(=O)N
OP0 326.3 Da LogP -2.69 TPSA 160.3 ✓ Ro5 ✓ Clean C1C[C@H](N(C[C@@H]1NOS(=O)(=O)O)C=O)C(=O)NOCCN
PBC 121.9 Da LogP -0.63 TPSA 40.5 ✓ Ro5 ✓ Clean B(c1ccccc1)(O)O
QFP 166.0 Da LogP -0.62 TPSA 49.7 ✓ Ro5 ✓ Clean B(c1ccccc1)(O)OCCO
QFS 196.0 Da LogP -0.61 TPSA 58.9 ✓ Ro5 ✓ Clean B(c1cccc(c1)OC)(O)OCCO
S1Y 377.5 Da LogP -1.46 TPSA 145.1 ✓ Ro5 ✓ Clean C1C[C@@H](CC[N@](C1)CCN)NC(=O)N2CC[C@H]([C@H]2C…
ZX0 350.4 Da LogP -1.24 TPSA 148.1 ✓ Ro5 ✓ Clean C1C[C@@H](CCNC1)NC(=O)N2CC[C@H]([C@H]2C(=O)O)NS…
ZX1 350.4 Da LogP -1.24 TPSA 148.1 ✓ Ro5 ✓ Clean C1C[C@H](CCNC1)NC(=O)N2CC[C@H]([C@H]2C(=O)O)NS(…

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.