Target Pathogen

Overview

Basic information about this protein and its source genome.

Accession: VK055_2340
Assembly: Klebsiella pneumoniae subsp. pneumoniae strain ATCC 43816 KPPR1, complete genome
Gene: AIK80943.1
Status: annotated
Amino acids: 351
Structure source: AlphaFold + ColabFold

EC

4.2.2.n1

GO

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: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:0005886 The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins. GO:0008932 Catalysis of the endolytic cleavage of the (1->4)-beta-glycosidic linkage between N-acetylmuramic acid (MurNAc) and N-acetylglucosamine (GlcNAc) residues in peptidoglycan with concomitant formation of a 1,6-anhydrobond in the MurNAc residue. 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.

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 (%): 44.928
Localization: Unknown
ColabFold pLDDT: 84.49

Selected Druggability evidence

AlphaFold / UniProt model

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 0.379

Structure A0A0H3GN20

Pocket Pocket 3

P2Rank 0.427

Structure A0A0H3GN20

Pocket Pocket 1

ColabFold model

FPocket 0.357 · Pocket 26

P2Rank 0.264 · Pocket 1

Core conservation Accessory gene

Roary core

CoreCruncher accessory

Gut microbiome 93 / 4744 genomes with a hit

Normalized 0.02

Sequence

Primary amino-acid sequence viewer.

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 6 GO

Enzyme Commission (EC)

1

4.2.2.n1

Gene 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: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:0005886 The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.
GO:0008932 Catalysis of the endolytic cleavage of the (1->4)-beta-glycosidic linkage between N-acetylmuramic acid (MurNAc) and N-acetylglucosamine (GlcNAc) residues in peptidoglycan with concomitant formation of a 1,6-anhydrobond in the MurNAc residue.
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.

40 records

Show feature table

Start	End	DB	Term	Name
28	37	Phobius	SIGNAL_PEPTIDE_C_REGION	C-terminal region of a signal peptide.
240	283	ProSiteProfiles	PS51782	LysM domain profile.
240	283	InterPro	IPR018392	LysM domain
38	351	Phobius	NON_CYTOPLASMIC_DOMAIN	Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
151	295	PANTHER	PTHR33734	LYSM DOMAIN-CONTAINING GPI-ANCHORED PROTEIN 2
299	342	SUPERFAMILY	SSF54106	LysM domain
299	342	InterPro	IPR036779	LysM domain superfamily
1	149	FunFam	G3DSA:1.10.530.10:FF:000004	Membrane-bound lytic murein transglycosylase D
242	283	Pfam	PF01476	LysM domain
242	283	InterPro	IPR018392	LysM domain
301	341	Pfam	PF01476	LysM domain
301	341	InterPro	IPR018392	LysM domain
241	284	SMART	SM00257	LysM_2
241	284	InterPro	IPR018392	LysM domain
300	342	SMART	SM00257	LysM_2
300	342	InterPro	IPR018392	LysM domain
240	283	SUPERFAMILY	SSF54106	LysM domain
240	283	InterPro	IPR036779	LysM domain superfamily
2	149	SUPERFAMILY	SSF53955	Lysozyme-like
2	149	InterPro	IPR023346	Lysozyme-like domain superfamily
1	37	Phobius	SIGNAL_PEPTIDE	Signal peptide region
299	343	ProSiteProfiles	PS51782	LysM domain profile.
299	343	InterPro	IPR018392	LysM domain
17	27	Phobius	SIGNAL_PEPTIDE_H_REGION	Hydrophobic region of a signal peptide.
8	138	CDD	cd16894	MltD-like
20	48	ProSitePatterns	PS00922	Prokaryotic transglycosylases signature.
20	48	InterPro	IPR000189	Prokaryotic transglycosylase, active site
2	150	Gene3D	G3DSA:1.10.530.10	-
239	284	FunFam	G3DSA:3.10.350.10:FF:000004	Membrane-bound lytic murein transglycosylase D
1	16	Phobius	SIGNAL_PEPTIDE_N_REGION	N-terminal region of a signal peptide.
299	341	CDD	cd00118	LysM
299	341	InterPro	IPR018392	LysM domain
297	344	FunFam	G3DSA:3.10.350.10:FF:000003	Membrane-bound lytic murein transglycosylase D
240	283	CDD	cd00118	LysM
297	344	Gene3D	G3DSA:3.10.350.10	LysM domain
297	344	InterPro	IPR036779	LysM domain superfamily
238	290	Gene3D	G3DSA:3.10.350.10	LysM domain
238	290	InterPro	IPR036779	LysM domain superfamily
1	113	Pfam	PF01464	Transglycosylase SLT domain
1	113	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...

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Structural evidence

0 + 2

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

Entry	Method	Resolution	Chain	Coverage	Links	Status
AlphaFold AF_A0A0H3GN20	AlphaFold	—	—	full sequence	—	Viewing
ColabFold VK055_2340	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
8				0.05
22				0.008
25				0.005
4				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	Score	Probability
1	9.3	0.427
2	2.0	0.036
3	1.79	0.028
4	1.3	0.012
5	1.15	0.008

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
4				0.053
18				0.01
2				0.003
3				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	Score	Probability
1	6.31	0.264
2	1.87	0.031
3	1.7	0.024
4	1.62	0.021
5	1.17	0.009

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.

2 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.

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
BUL	6FCQ	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…`

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
ZINC34074657	0.769	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…`

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.

VK055_2340

Overview

Target profile

Selected Druggability evidence

Sequence

Functional Annotations

Enzyme Commission (EC)

Gene Ontology (GO)

Sequence Features

3D Structure

Structural evidence

Pockets (FPOCKET)

Pockets (P2RANK)

Pockets (FPOCKET)

Pockets (P2RANK)

Ligand evidence