Protein profile
VK055_2584
soluble lytic murein transglycosylase
Genome: KpATCC43816
Overview
Basic information about this protein and its source genome.
- Accession
- VK055_2584
- Gene
- slt AIK81181.1
- Status
- annotated
- Amino acids
- 645
- 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)
- N
- DEG identity (%)
- 38.36
- Localization
- Periplasmic
- ColabFold pLDDT
- 94.15
Selected Druggability evidence
AlphaFold / UniProt modelSelected 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.
Sequence
Primary amino-acid sequence viewer.
Functional Annotations
Enzyme classification and Gene Ontology terms linked to this protein.
Enzyme Commission (EC)
1Gene Ontology (GO)
6- GO:0016020 A lipid bilayer along with all the proteins and protein complexes embedded in it and attached to it.
- 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:0042597 The region between the inner (cytoplasmic) and outer membrane (Gram-negative Bacteria) or cytoplasmic membrane and cell wall (Fungi and Gram-positive Bacteria).
- GO:0004553 Catalysis of the hydrolysis of any O-glycosyl bond.
- GO:0008933 Catalysis of the cleavage of a peptidoglycan chain into a peptidoglycan chain with N-acetyl-1,6-anhydromuramyl-[peptide] at the reducing end + a peptidoglycan chain with N-acetylglucosamine at the non-reducing end. Includes endolytic transglycosylase activity that fragments the glycan chain internally and exolytic transgylcosylase activity that cleaves a terminal disaccharide from the end of the glycan strand.
- 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.
Sequence Features
Domain/signature hits from InterPro and related databases.
Show feature table
| Start | End | DB | Term | Name |
|---|---|---|---|---|
| 1 | 27 | SignalP_GRAM_POSITIVE | SignalP-TM | SignalP-TM |
| 1 | 10 | Phobius | SIGNAL_PEPTIDE_N_REGION | N-terminal region of a signal peptide. |
| 407 | 472 | Pfam | PF14718 | Soluble lytic murein transglycosylase L domain |
| 407 | 472 | InterPro | IPR012289 | Lytic transglycosylase, superhelical linker |
| 479 | 641 | SUPERFAMILY | SSF53955 | Lysozyme-like |
| 479 | 641 | InterPro | IPR023346 | Lysozyme-like domain superfamily |
| 1 | 27 | Phobius | SIGNAL_PEPTIDE | Signal peptide region |
| 28 | 645 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. |
| 23 | 27 | Phobius | SIGNAL_PEPTIDE_C_REGION | C-terminal region of a signal peptide. |
| 1 | 27 | SignalP_EUK | SignalP-noTM | SignalP-noTM |
| 473 | 645 | Gene3D | G3DSA:1.10.530.10 | - |
| 10 | 645 | PANTHER | PTHR37423 | SOLUBLE LYTIC MUREIN TRANSGLYCOSYLASE-RELATED |
| 475 | 627 | CDD | cd13401 | Slt70-like |
| 11 | 22 | Phobius | SIGNAL_PEPTIDE_H_REGION | Hydrophobic region of a signal peptide. |
| 28 | 389 | Gene3D | G3DSA:1.25.20.10 | Bacterial muramidases |
| 403 | 472 | Gene3D | G3DSA:1.10.1240.20 | Lytic transglycosylase, superhelical linker domain |
| 403 | 472 | InterPro | IPR037061 | Lytic transglycosylase, superhelical linker domain superfamily |
| 28 | 477 | SUPERFAMILY | SSF48435 | Bacterial muramidases |
| 28 | 477 | InterPro | IPR008939 | Lytic transglycosylase, superhelical U-shaped |
| 501 | 529 | ProSitePatterns | PS00922 | Prokaryotic transglycosylases signature. |
| 501 | 529 | InterPro | IPR000189 | Prokaryotic transglycosylase, active site |
| 489 | 595 | Pfam | PF01464 | Transglycosylase SLT domain |
| 489 | 595 | InterPro | IPR008258 | Transglycosylase SLT domain 1 |
3D Structure
Selected loaded structure. Experimental PDB entries may cover only a portion of the sequence; predicted models typically cover the full protein.
Loading 3D structure...
Structural evidence
0 + 2Experimental PDB entries and predicted models. Click Switch to display a different structure in the viewer.
| Entry | Method | Resolution | Chain | Coverage | Links | Status |
|---|---|---|---|---|---|---|
|
AlphaFold
AF_A0A0H3GIW3
|
AlphaFold | — | — | full sequence | — | Viewing |
|
ColabFold
VK055_2584
|
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 |
|---|---|---|---|---|---|---|---|
| 6 | 0.349 | ||||||
| 15 | 0.001 | ||||||
| 16 | 0.001 | ||||||
| 9 | 0.0 |
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 | 12.12 | 0.553 | ||||||
| 2 | 6.05 | 0.248 | ||||||
| 3 | 5.45 | 0.214 | ||||||
| 4 | 4.01 | 0.13 | ||||||
| 5 | 3.32 | 0.093 |
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 |
|---|---|---|---|---|---|---|---|
| 3 | 0.756 | ||||||
| 44 | 0.628 | ||||||
| 8 | 0.002 | ||||||
| 2 | 0.001 |
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 | 8.45 | 0.384 | ||||||
| 2 | 6.14 | 0.253 | ||||||
| 3 | 5.62 | 0.224 | ||||||
| 4 | 4.99 | 0.186 | ||||||
| 5 | 3.43 | 0.098 |
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.
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.
No PDB structure with a co-crystallized ligand found for this exact protein.
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.
| Ligand | Source crystal | UniProt (homolog) | MW · LogP · TPSA | Lipinski | PAINS | SMILES |
|---|---|---|---|---|---|---|
| BLG | P0AGC3 | 552.6 Da LogP -6.16 TPSA 271.9 | 3 viol. | ✓ Clean |
CC(=O)N[C@@H]1[C@H]([C@@H]([C@H](O[C@H]1O[C@H]2…
|
|
| BUL | Q9HZI6 | 551.5 Da LogP -5.13 TPSA 267.3 | 3 viol. | ✓ Clean |
CC(=O)N[C@@H]1[C@H]([C@@H]([C@H](O[C@H]1O[C@H]2…
|
|
| NHE | Q9JXP1 | 207.3 Da LogP 0.80 TPSA 66.4 | ✓ Ro5 | ✓ Clean |
C1CCC(CC1)NCCS(=O)(=O)O
|
Experimental bioactivity from ChEMBL measured directly on this protein. Score = pchembl (−log Ki/IC₅₀; higher = more potent).
No ChEMBL bioactivity data found for this exact protein.
Bioactivity inferred from similar proteins in ChEMBL. Score = pchembl (−log Ki/IC₅₀; higher = more potent).
No ChEMBL hits found through similar proteins.
Proposed virtual-screening candidates from ZINC. Score = Tanimoto similarity to a known binder (0–1; higher = more similar).
| Ligand | Tanimoto | MW · LogP · TPSA | Lipinski | PAINS | SMILES |
|---|---|---|---|---|---|
| ZINC1710230 | 1.000 | 207.3 Da LogP 0.80 TPSA 66.4 | ✓ Ro5 | ✓ Clean |
O=S(=O)(O)CCNC1CCCCC1
|
| ZINC2004372 | 0.786 | 221.3 Da LogP 1.19 TPSA 66.4 | ✓ Ro5 | ✓ Clean |
O=S(=O)(O)CCCNC1CCCCC1
|
| ZINC38364153 | 0.786 | 235.3 Da LogP 1.58 TPSA 66.4 | ✓ Ro5 | ✓ Clean |
O=S(=O)(O)CCCCNC1CCCCC1
|
| ZINC34074657 | 0.562 | 444.4 Da LogP -4.05 TPSA 221.2 | 2 viol. | ✓ Clean |
CC(=O)N[C@H]1[C@H](O[C@H]2C[C@@H](C(=O)O)N[C@@H…
|
| ZINC19367005 | 0.560 | 224.4 Da LogP 2.83 TPSA 24.1 | ✓ Ro5 | ✓ Clean |
C1CCC(NCCNC2CCCCC2)CC1
|
| ZINC26468763 | 0.559 | 243.3 Da LogP -1.35 TPSA 100.5 | ✓ Ro5 | ✓ Clean |
O=S(=O)(O)CCN[C@@H]1CCS(=O)(=O)C1
|
| ZINC26468770 | 0.559 | 243.3 Da LogP -1.35 TPSA 100.5 | ✓ Ro5 | ✓ Clean |
O=S(=O)(O)CCN[C@H]1CCS(=O)(=O)C1
|
| ZINC5188799 | 0.556 | 280.5 Da LogP 4.39 TPSA 24.1 | ✓ Ro5 | ✓ Clean |
C(CCCNC1CCCCC1)CCNC1CCCCC1
|
| ZINC2168583 | 0.529 | 237.3 Da LogP 0.16 TPSA 86.6 | ✓ Ro5 | ✓ Clean |
O=S(=O)(O)C[C@@H](O)CNC1CCCCC1
|
| ZINC2168584 | 0.529 | 237.3 Da LogP 0.16 TPSA 86.6 | ✓ Ro5 | ✓ Clean |
O=S(=O)(O)C[C@H](O)CNC1CCCCC1
|
| ZINC130127586 | 0.515 | 260.4 Da LogP 1.38 TPSA 58.2 | ✓ Ro5 | ✓ Clean |
O=S(=O)(NCCNC1CCCCCC1)C1CC1
|
| ZINC78421079 | 0.515 | 210.3 Da LogP 1.43 TPSA 41.1 | ✓ Ro5 | ✓ Clean |
O=C(NCCNC1CCCCC1)C1CC1
|
| ZINC122239480 | 0.500 | 238.4 Da LogP 2.22 TPSA 41.1 | ✓ Ro5 | ✓ Clean |
O=C(NCCNC1CCCCCC1)C1CCC1
|
| ZINC165485 | 0.500 | 301.8 Da LogP 3.04 TPSA 46.2 | ✓ Ro5 | ✓ Clean |
O=S(=O)(CCNC1CCCCC1)c1ccc(Cl)cc1
|
| ZINC38889906 | 0.500 | 226.4 Da LogP 3.21 TPSA 38.0 | ✓ Ro5 | ✓ Clean |
NCCNC1CCCCCCCCCCC1
|
| ZINC60934954 | 0.500 | 315.9 Da LogP 3.43 TPSA 46.2 | ✓ Ro5 | ✓ Clean |
O=S(=O)(CCNC1CCCCCC1)c1ccc(Cl)cc1
|
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.