Protein profile

PA4418

penicillin-binding protein 3

Genome: NC_002516.2

Gene: L4V69_30060 IPC1295_15535 pbpB GUL26_13375 ftsI_1 ftsI ALP65_00912 PA4418 GNQ48_11285 PAERUG_P19_London_7_VIM_2_05_10_00246 CAZ10_21230 Structure source: Experimental + AlphaFold UniProt G3XD46 UniProt Q51504
Amino acids 579
Annotations 12
Features 21
PDB binders 25
Druggability 0.649

Overview

Basic information about this protein and its source genome.

Accession
PA4418
Gene
L4V69_30060 IPC1295_15535 pbpB GUL26_13375 ftsI_1 ftsI ALP65_00912 PA4418 GNQ48_11285 PAERUG_P19_London_7_VIM_2_05_10_00246 CAZ10_21230
Status
annotated
Amino acids
579
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 0.649
Structure
Pocket

Sequence

Primary amino-acid sequence viewer.

MKLNYFQGALYPWRFCVIVGLLLAMVGAIVWRIVDLHVIDHDFLKGQGDARSVRHIAIPAHRGLITDRNGEPLAVSTPVTTLWANPKELMTAKERWPQLAAALGQDTKLFADRIEQNAEREFIYLVRGLTPEQGEGVIALKVPGVYSIEEFRRFYPAGEVVAHAVGFTDVDDRGREGIELAFDEWLAGVPGKRQVLKDRRGRVIKDVQVTKNAKPGKTLALSIDLRLQYLAHRELRNALLENGAKAGSLVIMDVKTGEILAMTNQPTYNPNNRRNLQPAAMRNRAMIDVFEPGSTVKPFSMSAALASGRWKPSDIVDVYPGTLQIGRYTIRDVSRNSRQLDLTGILIKSSNVGISKIAFDIGAESIYSVMQQVGLGQDTGLGFPGERVGNLPNHRKWPKAETATLAYGYGLSVTAIQLAHAYAALANDGKSVPLSMTRVDRVPDGVQVISPEVASTVQGMLQQVVEAQGGVFRAQVPGYHAAGKSGTARKVSVGTKGYRENAYRSLFAGFAPATDPRIAMVVVIDEPSKAGYFGGLVSAPVFSKVMAGALRLMNVPPDNLPTATEQQQVNAAPAKGGRG

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 11 GO

Enzyme Commission (EC)

1

Gene Ontology (GO)

11
  • 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:0008955 Catalysis of the reaction: [GlcNAc-(1->4)-Mur2Ac(oyl-L-Ala-gamma-D-Glu-L-Lys-D-Ala-D-Ala)](n)-di-trans,octa-cis-undecaprenyl diphosphate + beta-D-GlcNAc-(1->4)-Mur2Ac(oyl-L-Ala-gamma-D-Glu-L-Lys-D-Ala-D-Ala)-di-trans,octa-cis-undecaprenyl diphosphate = [GlcNAc-(1->4)-Mur2Ac(oyl-L-Ala-gamma-D-Glu-L-Lys-D-Ala-D-Ala)](n+1)-di-trans-octa-cis-undecaprenyl diphosphate + di-trans,octa-cis-undecaprenyl diphosphate + H+.
  • 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:0000917 The assembly and arrangement of a septum that spans the plasma membrane interface between progeny cells following cytokinesis. The progeny cells that form a division septum are not able to exchange intracellular material.
  • GO:0043093 A cytokinesis process that involves a set of conserved proteins including FtsZ, and results in the formation of two similarly sized and shaped cells.
  • 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:0051301 The process resulting in division and partitioning of components of a cell to form more cells; may or may not be accompanied by the physical separation of a cell into distinct, individually membrane-bounded daughter cells.

Sequence Features

Domain/signature hits from InterPro and related databases.

21 records
Show feature table
Start End DB Term Name
12 34 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
247 546 Pfam PF00905 Penicillin binding protein transpeptidase domain
247 546 InterPro IPR001460 Penicillin-binding protein, transpeptidase
11 559 PANTHER PTHR30627 PEPTIDOGLYCAN D,D-TRANSPEPTIDASE
50 221 Gene3D G3DSA:3.90.1310.10 -
1 11 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
50 221 FunFam G3DSA:3.90.1310.10:FF:000003 Peptidoglycan D,D-transpeptidase FtsI
174 561 SUPERFAMILY SSF56601 beta-lactamase/transpeptidase-like
174 561 InterPro IPR012338 Beta-lactamase/transpeptidase-like
54 221 SUPERFAMILY SSF56519 Penicillin binding protein dimerisation domain
54 221 InterPro IPR036138 Penicillin-binding protein, dimerisation domain superfamily
35 579 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
4 575 Hamap MF_02080 Peptidoglycan D,D-transpeptidase FtsI [ftsI].
4 575 InterPro IPR037532 Peptidoglycan D,D-transpeptidase FtsI
223 550 Gene3D G3DSA:3.30.450.330 -
283 464 Gene3D G3DSA:3.40.710.10 -
283 464 InterPro IPR012338 Beta-lactamase/transpeptidase-like
12 34 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
558 579 MobiDBLite mobidb-lite consensus disorder prediction
58 207 Pfam PF03717 Penicillin-binding Protein dimerisation domain
58 207 InterPro IPR005311 Penicillin-binding protein, dimerisation domain

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

56 + 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 7KIT
X-ray 2.09 Å A
100.0% 1-579
Viewing
PDB 7KIV
X-ray 2.39 Å A
100.0% 1-579
Loaded
PDB 7KIW
X-ray 2.49 Å A
100.0% 1-579
Loaded
PDB 3OC2
X-ray 1.97 Å A
94.1% 35-579
Loaded
PDB 5DF7
X-ray 2.00 Å A,B
94.1% 35-579
Loaded
PDB 5DF8
X-ray 2.00 Å A,B
94.1% 35-579
Loaded
PDB 4KQR
X-ray 2.01 Å A,B
94.1% 35-579
Loaded
PDB 4KQQ
X-ray 2.10 Å A,B
94.1% 35-579
Loaded
PDB 3OCL
X-ray 2.30 Å A
94.1% 35-579
Loaded
PDB 4KQO
X-ray 2.31 Å A,B
94.1% 35-579
Loaded
PDB 3OCN
X-ray 2.61 Å A
94.1% 35-579
Loaded
PDB 5DF9
X-ray 2.70 Å A
94.1% 35-579
Loaded
PDB 6HR6
X-ray 2.53 Å A
92.1% 47-579
Loaded
PDB 6HR4
X-ray 1.19 Å A
91.5% 50-579
Loaded
PDB 6HZR
X-ray 1.19 Å A
91.5% 50-579
Loaded
PDB 7AU1
X-ray 1.36 Å A
91.5% 50-579
Loaded
PDB 7ATW
X-ray 1.44 Å A
91.5% 50-579
Loaded
PDB 7ATM
X-ray 1.58 Å A
91.5% 50-579
Loaded
PDB 7ATO
X-ray 1.59 Å A
91.5% 50-579
Loaded
PDB 3PBT
X-ray 1.64 Å A
91.5% 50-579
Loaded
PDB 6I1E
X-ray 1.64 Å A
91.5% 50-579
Loaded
PDB 3PBQ
X-ray 1.70 Å A
91.5% 50-579
Loaded
PDB 6R42
X-ray 1.72 Å A
91.5% 50-579
Loaded
PDB 3PBO
X-ray 1.74 Å A
91.5% 50-579
Loaded
PDB 6VJE
X-ray 1.76 Å A
91.5% 50-579
Loaded
PDB 7ATX
X-ray 1.79 Å A
91.5% 50-579
Loaded
PDB 7AU8
X-ray 1.79 Å A
91.5% 50-579
Loaded
PDB 6UN3
X-ray 1.90 Å A
91.5% 50-579
Loaded
PDB 7AUB
X-ray 1.91 Å A
91.5% 50-579
Loaded
PDB 3PBR
X-ray 1.95 Å A
91.5% 50-579
Loaded
PDB 6HR9
X-ray 1.99 Å A
91.5% 50-579
Loaded
PDB 3PBN
X-ray 2.00 Å A
91.5% 50-579
Loaded
PDB 3PBS
X-ray 2.00 Å A
91.5% 50-579
Loaded
PDB 7LC4
X-ray 2.00 Å A
91.5% 50-579
Loaded
PDB 7AUH
X-ray 2.01 Å A
91.5% 50-579
Loaded
PDB 4L0L
X-ray 2.10 Å A
91.5% 50-579
Loaded
PDB 7AU9
X-ray 2.14 Å A
91.5% 50-579
Loaded
PDB 7AU0
X-ray 2.17 Å A
91.5% 50-579
Loaded
PDB 4FSF
X-ray 2.20 Å A
91.5% 50-579
Loaded
PDB 6R40
X-ray 2.20 Å A
91.5% 50-579
Loaded
PDB 7JWL
X-ray 2.20 Å A
91.5% 50-579
Loaded
PDB 7LY1
X-ray 2.20 Å A
91.5% 50-579
Loaded
PDB 6UN1
X-ray 2.26 Å A
91.5% 50-579
Loaded
PDB 6VOT
X-ray 2.40 Å A
91.5% 50-579
Loaded
PDB 7ONK
X-ray 1.73 Å A,B
90.7% 39-563
Loaded
PDB 7ONY
X-ray 1.77 Å A
90.7% 39-563
Loaded
PDB 7ONZ
X-ray 1.86 Å A
90.7% 39-563
Loaded
PDB 7ONX
X-ray 2.16 Å A
90.7% 39-563
Loaded
PDB 6Y6U
X-ray 1.55 Å A
88.8% 50-563
Loaded
PDB 6R3X
X-ray 1.59 Å A
88.8% 50-563
Loaded
PDB 6Y6Z
X-ray 1.70 Å A
88.8% 50-563
Loaded
PDB 9FZ7
X-ray 1.80 Å A
88.3% 52-562
Loaded
PDB 9FZO
X-ray 1.80 Å A
88.3% 52-562
Loaded
PDB 9FZE
X-ray 2.10 Å A
88.3% 52-562
Loaded
PDB 9FZ8
X-ray 2.11 Å A
88.3% 52-562
Loaded
PDB 9FZP
X-ray 2.70 Å A
88.3% 52-562
Loaded
AlphaFold PA4418
AlphaFold full sequence Loaded
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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.

76 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
0W0 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 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 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 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 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 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 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 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 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…
IM2 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 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 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…
ODZ 263.3 Da LogP 1.47 TPSA 86.6 ✓ Ro5 ✓ Clean C[C@](CC(=C)O)(C=O)NC(=O)Cc1ccc(cc1)O
OEE 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 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 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 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 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 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 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 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.