Protein profile

KP13_00397

Lytic transglycosylase protein

Genome: KpKP13

Gene: AHE46865.1 Structure source: AlphaFold + ColabFold UniProt A0A0H3GLY4

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Amino acids 526

Annotations 0

Features 23

PDB binders 3

Druggability 0.66

Overview

Basic information about this protein and its source genome.

Accession: KP13_00397
Assembly: Klebsiella pneumoniae subsp. pneumoniae Kp13, complete sequence
Gene: AHE46865.1
Status: annotated
Amino acids: 526
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 (%): 0.0
Localization: Cytoplasmic
ColabFold pLDDT: 84.24

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 0.66

Structure A0A0H3GLY4

Pocket Pocket 4

P2Rank 0.683

Structure A0A0H3GLY4

Pocket Pocket 1

ColabFold model

FPocket 0.633 · Pocket 7

P2Rank 0.767 · Pocket 1

Core conservation Accessory gene

Roary accessory

CoreCruncher accessory

Gut microbiome 17 / 4744 genomes with a hit

Normalized 0.004

Sequence

Primary amino-acid sequence viewer.

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

No GO or EC annotations are currently loaded for this protein.

Sequence Features

Domain/signature hits from InterPro and related databases.

23 records

Show feature table

Start	End	DB	Term	Name
336	484	CDD	cd13403	MLTF-like
32	526	Phobius	NON_CYTOPLASMIC_DOMAIN	Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
66	312	CDD	cd01009	PBP2_YfhD_N
330	501	Gene3D	G3DSA:1.10.530.10	-
1	10	Phobius	SIGNAL_PEPTIDE_N_REGION	N-terminal region of a signal peptide.
335	445	Pfam	PF01464	Transglycosylase SLT domain
335	445	InterPro	IPR008258	Transglycosylase SLT domain 1
1	31	Phobius	SIGNAL_PEPTIDE	Signal peptide region
7	29	TMHMM	TMhelix	Region of a membrane-bound protein predicted to be embedded in the membrane.
166	270	Gene3D	G3DSA:3.40.190.10	-
67	314	SMART	SM00062	AABind_6
67	314	InterPro	IPR001638	Solute-binding protein family 3/N-terminal domain of MltF
114	302	Pfam	PF00497	Bacterial extracellular solute-binding proteins, family 3
114	302	InterPro	IPR001638	Solute-binding protein family 3/N-terminal domain of MltF
67	302	SUPERFAMILY	SSF53850	Periplasmic binding protein-like II
1	31	SignalP_GRAM_POSITIVE	SignalP-TM	SignalP-TM
332	486	SUPERFAMILY	SSF53955	Lysozyme-like
332	486	InterPro	IPR023346	Lysozyme-like domain superfamily
64	303	Gene3D	G3DSA:3.40.190.10	-
1	31	SignalP_EUK	SignalP-noTM	SignalP-noTM
27	31	Phobius	SIGNAL_PEPTIDE_C_REGION	C-terminal region of a signal peptide.
11	26	Phobius	SIGNAL_PEPTIDE_H_REGION	Hydrophobic region of a signal peptide.
8	302	PANTHER	PTHR35936	MEMBRANE-BOUND LYTIC MUREIN TRANSGLYCOSYLASE F

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_A0A0H3GLY4	AlphaFold	—	—	full sequence	—	Viewing
ColabFold KP13_00397	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
4				0.66
35				0.3

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	10.41	0.559
2	8.08	0.43
3	4.05	0.162
4	2.99	0.098
5	2.4	0.064

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
7				0.633
35				0.531
4				0.528

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	11.78	0.625
2	9.33	0.501
3	4.1	0.165
4	2.75	0.083
5	2.53	0.071

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.

52 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
6X4	5AA4	A0A1I9GEN8	489.6 Da LogP -3.89 TPSA 244.7	1 viol.	✓ Clean	`C[C@H](C(=O)N)NC(=O)C(CCCC[NH3+])NC(=O)CC[C@H](…`
BLG	1SLY	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	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…`
ZINC15722130	0.582	488.5 Da LogP -2.61 TPSA 243.0	1 viol.	✓ Clean	`C[C@H](N)C(=O)N[C@H](CCC(=O)N[C@@H](CCCCN)C(=O)…`
ZINC255987061	0.582	488.5 Da LogP -2.61 TPSA 243.0	1 viol.	✓ Clean	`C[C@H](N)C(=O)N[C@H](CCC(=O)N[C@H](CCCCN)C(=O)N…`
ZINC255987062	0.582	488.5 Da LogP -2.61 TPSA 243.0	1 viol.	✓ Clean	`C[C@H](N)C(=O)N[C@H](CCC(=O)N[C@H](CCCCN)C(=O)N…`
ZINC255987063	0.582	488.5 Da LogP -2.61 TPSA 243.0	1 viol.	✓ Clean	`C[C@H](N)C(=O)N[C@H](CCC(=O)N[C@H](CCCCN)C(=O)N…`
ZINC255987064	0.582	488.5 Da LogP -2.61 TPSA 243.0	1 viol.	✓ Clean	`C[C@H](N)C(=O)N[C@H](CCC(=O)N[C@H](CCCCN)C(=O)N…`
ZINC64219359	0.565	202.3 Da LogP -0.41 TPSA 106.4	✓ Ro5	✓ Clean	`CC(C)[C@H](C(=O)[C@@H](C)N)[C@H](N)C(=O)O`
ZINC64219360	0.565	202.3 Da LogP -0.41 TPSA 106.4	✓ Ro5	✓ Clean	`CC(C)[C@@H](C(=O)[C@@H](C)N)[C@H](N)C(=O)O`
ZINC79670384	0.565	202.3 Da LogP -0.41 TPSA 106.4	✓ Ro5	✓ Clean	`CC(C)[C@@H](C(=O)[C@H](C)N)[C@H](N)C(=O)O`
ZINC79670387	0.565	202.3 Da LogP -0.41 TPSA 106.4	✓ Ro5	✓ Clean	`CC(C)[C@H](C(=O)[C@H](C)N)[C@H](N)C(=O)O`
ZINC5131766	0.538	224.3 Da LogP -1.26 TPSA 92.4	✓ Ro5	✓ Clean	`N[C@@H](CS)C(=O)N[C@@H](CS)C(=O)O`
ZINC13529436	0.533	212.3 Da LogP 1.76 TPSA 46.3	✓ Ro5	✓ Clean	`CC[C@H](C)[C@H](N)C(=O)N1CCCCCC1`
ZINC19502834	0.533	212.3 Da LogP 1.76 TPSA 46.3	✓ Ro5	✓ Clean	`CC[C@@H](C)[C@@H](N)C(=O)N1CCCCCC1`
ZINC19502836	0.533	212.3 Da LogP 1.76 TPSA 46.3	✓ Ro5	✓ Clean	`CC[C@H](C)[C@@H](N)C(=O)N1CCCCCC1`
ZINC19502838	0.533	212.3 Da LogP 1.76 TPSA 46.3	✓ Ro5	✓ Clean	`CC[C@@H](C)[C@H](N)C(=O)N1CCCCCC1`
ZINC2560328	0.520	239.1 Da LogP 1.53 TPSA 63.3	✓ Ro5	✓ Clean	`N[C@@H](CC(C(F)(F)F)C(F)(F)F)C(=O)O`
ZINC4348166	0.520	239.1 Da LogP 1.53 TPSA 63.3	✓ Ro5	✓ Clean	`N[C@H](CC(C(F)(F)F)C(F)(F)F)C(=O)O`
ZINC1579628	0.517	202.3 Da LogP -0.05 TPSA 92.4	✓ Ro5	✓ Clean	`CC(C)C[C@@H](N)C(=O)NCCC(=O)O`
ZINC2390984	0.517	202.3 Da LogP -0.05 TPSA 92.4	✓ Ro5	✓ Clean	`CC(C)C[C@H](N)C(=O)NCCC(=O)O`
ZINC11959312	0.516	213.3 Da LogP 0.13 TPSA 49.6	✓ Ro5	✓ Clean	`CC[C@@H](C)[C@H](N)C(=O)N1CCN(C)CC1`
ZINC11959315	0.516	213.3 Da LogP 0.13 TPSA 49.6	✓ Ro5	✓ Clean	`CC[C@H](C)[C@H](N)C(=O)N1CCN(C)CC1`
ZINC19504598	0.516	213.3 Da LogP 0.13 TPSA 49.6	✓ Ro5	✓ Clean	`CC[C@@H](C)[C@@H](N)C(=O)N1CCN(C)CC1`
ZINC19504599	0.516	213.3 Da LogP 0.13 TPSA 49.6	✓ Ro5	✓ Clean	`CC[C@H](C)[C@@H](N)C(=O)N1CCN(C)CC1`
ZINC247966296	0.510	290.3 Da LogP -1.40 TPSA 136.0	✓ Ro5	✓ Clean	`C[C@H](O)C(=O)NCCCC[C@H](NC(=O)[C@H](C)O)C(=O)O`
ZINC247966298	0.510	290.3 Da LogP -1.40 TPSA 136.0	✓ Ro5	✓ Clean	`C[C@H](O)C(=O)NCCCC[C@@H](NC(=O)[C@@H](C)O)C(=O…`
ZINC247966301	0.510	290.3 Da LogP -1.40 TPSA 136.0	✓ Ro5	✓ Clean	`C[C@H](O)C(=O)NCCCC[C@@H](NC(=O)[C@H](C)O)C(=O)O`
ZINC247966305	0.510	290.3 Da LogP -1.40 TPSA 136.0	✓ Ro5	✓ Clean	`C[C@H](O)C(=O)NCCCC[C@H](NC(=O)[C@@H](C)O)C(=O)O`
ZINC11959285	0.500	200.3 Da LogP 0.22 TPSA 55.6	✓ Ro5	✓ Clean	`CC[C@@H](C)[C@H](N)C(=O)N1CCOCC1`
ZINC11959288	0.500	200.3 Da LogP 0.22 TPSA 55.6	✓ Ro5	✓ Clean	`CC[C@H](C)[C@H](N)C(=O)N1CCOCC1`
ZINC11961470	0.500	200.3 Da LogP 1.52 TPSA 55.1	✓ Ro5	✓ Clean	`CC(C)CCNC(=O)[C@@H](N)CC(C)C`
ZINC1589383	0.500	244.3 Da LogP 0.98 TPSA 92.4	✓ Ro5	✓ Clean	`CC[C@@H](C)[C@H](NC(=O)[C@@H](N)CC(C)C)C(=O)O`
ZINC17142439	0.500	244.3 Da LogP 0.98 TPSA 92.4	✓ Ro5	✓ Clean	`CC[C@@H](C)[C@@H](NC(=O)[C@@H](N)CC(C)C)C(=O)O`
ZINC17142440	0.500	244.3 Da LogP 0.98 TPSA 92.4	✓ Ro5	✓ Clean	`CC[C@H](C)[C@@H](NC(=O)[C@@H](N)CC(C)C)C(=O)O`
ZINC19506206	0.500	200.3 Da LogP 0.22 TPSA 55.6	✓ Ro5	✓ Clean	`CC[C@@H](C)[C@@H](N)C(=O)N1CCOCC1`
ZINC19506207	0.500	200.3 Da LogP 0.22 TPSA 55.6	✓ Ro5	✓ Clean	`CC[C@H](C)[C@@H](N)C(=O)N1CCOCC1`
ZINC2390960	0.500	244.3 Da LogP 0.98 TPSA 92.4	✓ Ro5	✓ Clean	`CC[C@H](C)[C@H](NC(=O)[C@@H](N)CC(C)C)C(=O)O`
ZINC2522617	0.500	245.3 Da LogP -1.20 TPSA 135.5	✓ Ro5	✓ Clean	`CC(C)C[C@H](N)C(=O)N[C@@H](CC(N)=O)C(=O)O`
ZINC2562301	0.500	244.3 Da LogP 0.98 TPSA 92.4	✓ Ro5	✓ Clean	`CC[C@@H](C)[C@H](NC(=O)[C@H](N)CC(C)C)C(=O)O`
ZINC36158109	0.500	221.3 Da LogP 2.10 TPSA 52.3	✓ Ro5	✓ Clean	`CC[C@H](C)[C@H](N)C(=O)OCc1ccccc1`
ZINC36158113	0.500	221.3 Da LogP 2.10 TPSA 52.3	✓ Ro5	✓ Clean	`CC[C@@H](C)[C@@H](N)C(=O)OCc1ccccc1`
ZINC37246007	0.500	221.3 Da LogP 2.10 TPSA 52.3	✓ Ro5	✓ Clean	`CC[C@@H](C)[C@H](N)C(=O)OCc1ccccc1`
ZINC37246008	0.500	221.3 Da LogP 2.10 TPSA 52.3	✓ Ro5	✓ Clean	`CC[C@H](C)[C@@H](N)C(=O)OCc1ccccc1`
ZINC40439568	0.500	208.2 Da LogP -2.19 TPSA 112.7	✓ Ro5	✓ Clean	`N[C@@H](CS)C(=O)N[C@@H](CO)C(=O)O`
ZINC4556661	0.500	245.3 Da LogP -1.20 TPSA 135.5	✓ Ro5	✓ Clean	`CC(C)C[C@@H](N)C(=O)N[C@@H](CC(N)=O)C(=O)O`
ZINC4556662	0.500	245.3 Da LogP -1.20 TPSA 135.5	✓ Ro5	✓ Clean	`CC(C)C[C@H](N)C(=O)N[C@H](CC(N)=O)C(=O)O`
ZINC4556663	0.500	245.3 Da LogP -1.20 TPSA 135.5	✓ Ro5	✓ Clean	`CC(C)C[C@@H](N)C(=O)N[C@H](CC(N)=O)C(=O)O`
ZINC5618626	0.500	244.3 Da LogP 0.98 TPSA 92.4	✓ Ro5	✓ Clean	`CC[C@H](C)[C@H](NC(=O)[C@H](N)CC(C)C)C(=O)O`
ZINC5618627	0.500	244.3 Da LogP 0.98 TPSA 92.4	✓ Ro5	✓ Clean	`CC[C@@H](C)[C@@H](NC(=O)[C@H](N)CC(C)C)C(=O)O`
ZINC5618628	0.500	244.3 Da LogP 0.98 TPSA 92.4	✓ Ro5	✓ Clean	`CC[C@H](C)[C@@H](NC(=O)[C@H](N)CC(C)C)C(=O)O`

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.