Protein profile

PA4003

penicillin-binding protein 2

Genome: NC_002516.2

Gene: spoVD CAZ10_26315 PA4003 PAERUG_P19_London_7_VIM_2_05_10_06701 mrdA GNQ48_15490 IPC1295_14660 GUL26_00100 pbpA L4V69_08310 Structure source: Experimental + AlphaFold UniProt G3XCV7 UniProt Q9X6V3
Amino acids 646
Annotations 10
Features 21
PDB binders 23
Druggability 0.808

Overview

Basic information about this protein and its source genome.

Accession
PA4003
Gene
spoVD CAZ10_26315 PA4003 PAERUG_P19_London_7_VIM_2_05_10_06701 mrdA GNQ48_15490 IPC1295_14660 GUL26_00100 pbpA L4V69_08310
Status
annotated
Amino acids
646
Structure source
Experimental + AlphaFold

Target profile

Computed evidence for target prioritization.

Human off-target
No hit
Gut microbiome off-target
hit
Essential (DEG)
Y
Localization
CytoplasmicMembrane

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 0.808
Structure
Pocket

Sequence

Primary amino-acid sequence viewer.

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 9 GO

Enzyme Commission (EC)

1

Gene Ontology (GO)

9
  • 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:0071972 Catalysis of the reaction: 2 a peptidoglycan dimer (tetrapeptide) + 3 H2O = a peptidoglycan tetramer with L,D cross-links (L-Lys-D-Asn-L-Lys) + di-trans,poly-cis-undecaprenyl diphosphate + 4 D-alanine.
  • 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:0016020 A lipid bilayer along with all the proteins and protein complexes embedded in it and attached to it.

Sequence Features

Domain/signature hits from InterPro and related databases.

21 records
Show feature table
Start End DB Term Name
56 250 SUPERFAMILY SSF56519 Penicillin binding protein dimerisation domain
56 250 InterPro IPR036138 Penicillin-binding protein, dimerisation domain superfamily
85 161 Gene3D G3DSA:3.30.1390.30 -
19 607 NCBIfam TIGR03423 penicillin-binding protein 2
19 607 InterPro IPR017790 Penicillin-binding protein 2
3 611 Hamap MF_02081 Peptidoglycan D,D-transpeptidase MrdA [mrdA].
3 611 InterPro IPR017790 Penicillin-binding protein 2
251 607 SUPERFAMILY SSF56601 beta-lactamase/transpeptidase-like
251 607 InterPro IPR012338 Beta-lactamase/transpeptidase-like
64 246 Gene3D G3DSA:3.90.1310.10 -
268 604 Pfam PF00905 Penicillin binding protein transpeptidase domain
268 604 InterPro IPR001460 Penicillin-binding protein, transpeptidase
41 646 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
21 40 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
1 20 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
64 236 Pfam PF03717 Penicillin-binding Protein dimerisation domain
64 236 InterPro IPR005311 Penicillin-binding protein, dimerisation domain
21 40 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
250 622 Gene3D G3DSA:3.40.710.10 -
250 622 InterPro IPR012338 Beta-lactamase/transpeptidase-like
11 615 PANTHER PTHR30627 PEPTIDOGLYCAN D,D-TRANSPEPTIDASE

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

1 + 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 7KIS
X-ray 2.87 Å A,B
100.0% 1-646
Viewing
AlphaFold PA4003
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 0.463
3 0.443

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 7.56 0.399
2 2.0 0.043

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.

77 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
0W0 Q51504 672.6 Da LogP -2.06 TPSA 328.0 3 viol. ✓ Clean CC(C)(C(=O)O)O/N=C(/c1csc(n1)N)\C(=O)N[C@H](C=O…
59F Q51504 535.6 Da LogP -0.73 TPSA 185.4 1 viol. ✓ Clean CCN1CCN(C(=O)C1=O)C(=O)N[C@H](c2ccc(cc2)O)C(=O)…
59H Q51504 463.5 Da LogP 0.04 TPSA 156.9 ✓ Ro5 ✓ Clean CC1([C@@H](N[C@H](S1)[C@@H](C=O)NC(=O)[C@@H](c2…
59J Q51504 549.6 Da LogP -0.36 TPSA 206.0 1 viol. ✓ Clean CCN1CCN(C(=O)C1=O)C(=O)N[C@H](c2ccc(cc2)O)C(=O)…
AXL G3XD46 367.4 Da LogP -0.03 TPSA 141.8 ✓ Ro5 ✓ Clean CC1([C@@H](N[C@H](S1)[C@@H](C=O)NC(=O)[C@@H](c2…
AZR Q51504 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)/…
CAZ G3XD46 469.5 Da LogP 0.15 TPSA 193.6 1 viol. ✓ Clean CC(C)(C(=O)O)O/N=C(/c1csc(n1)N)\C(=O)N[C@H](C=O…
CB9 Q51504 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…
CTJ Q51504 549.6 Da LogP -0.02 TPSA 197.2 2 viol. ✓ Clean CC(C)(C(=O)O)O/N=C(/c1csc(n1)N)\C(=O)N[C@H](C=O…
ET5 P0AD65 334.3 Da LogP -0.93 TPSA 168.2 ✓ Ro5 ✓ Clean c1c(ocn1)C2=C[C@H](N(C[C@@H]2NOS(=O)(=O)O)C(=O)…
IM2 G3XD46 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…
JPP G3XD46 519.6 Da LogP -0.29 TPSA 165.2 1 viol. ✓ Clean CCN1CCN(C(=O)C1=O)C(=O)N[C@H](c2ccccc2)C(=O)N[C…
MER G3XD46 385.5 Da LogP -0.36 TPSA 119.0 ✓ Ro5 ✓ Clean C[C@@H]1[C@@H](NC(=C1S[C@H]2C[C@H](NC2)C(=O)N(C…
NXL P0AD65 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
ODZ G3XD46 263.3 Da LogP 1.47 TPSA 86.6 ✓ Ro5 ✓ Clean C[C@](CC(=C)O)(C=O)NC(=O)Cc1ccc(cc1)O
OEE G3XD46 229.3 Da LogP 1.93 TPSA 75.6 ✓ Ro5 ✓ Clean C[C@](CC(=C)O)(C=O)NC(=O)OC(C)(C)C
PFV Q51504 634.6 Da LogP -2.64 TPSA 314.0 3 viol. ✓ Clean CC(C)(C(=O)O)O/N=C(/c1csc(n1)N)\C(=O)N[C@H](C=O…
R7G G3XD46 688.6 Da LogP -2.02 TPSA 303.5 3 viol. Alert CC(C)(C(=O)O)O/N=C(/c1csc(n1)N)\C(=O)N[C@@H](CN…
RB6 Q47759 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]…
TJ7 G3XD46 416.5 Da LogP 0.47 TPSA 142.0 ✓ Ro5 ✓ Clean CC1([C@@H](N[C@H](S1)[C@@](C=O)(NC(=O)[C@@H](c2…
UE1 G3XD46 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]…
VPP G3XD46 535.6 Da LogP -0.41 TPSA 185.4 1 viol. ✓ Clean CCN1CCN(C(=O)C1=O)C(=O)N[C@H](c2ccccc2)C(=O)N[C…
XT8 G3XD46 386.5 Da LogP 0.49 TPSA 132.8 ✓ Ro5 ✓ Clean CC1([C@@H](N[C@H](S1)[C@@H](C=O)NC(=O)[C@@H](c2…

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.