Protein profile

VK055_4608

signal peptidase I

Genome: KpATCC43816

Gene: lepB AIK83142.1 Structure source: AlphaFold + ColabFold UniProt A0A0H3GTU0

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Amino acids 324

Annotations 8

Features 34

PDB binders 1

Druggability 0.733

Overview

Basic information about this protein and its source genome.

Accession: VK055_4608
Assembly: Klebsiella pneumoniae subsp. pneumoniae strain ATCC 43816 KPPR1, complete genome
Gene: lepB AIK83142.1
Status: annotated
Amino acids: 324
Structure source: AlphaFold + ColabFold

3.4.21.89

GO:0016020 A lipid bilayer along with all the proteins and protein complexes embedded in it and attached to it. GO:0006508 The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds. GO:0006465 OBSOLETE. The proteolytic removal of a signal peptide from a protein during or after transport to a specific location in the cell. GO:0008236 Catalysis of the hydrolysis of peptide bonds in a polypeptide chain by a catalytic mechanism that involves a catalytic triad consisting of a serine nucleophile that is activated by a proton relay involving an acidic residue (e.g. aspartate or glutamate) and a basic residue (usually histidine). GO:0004252 Catalysis of the hydrolysis of internal, alpha-peptide bonds in a polypeptide chain by a catalytic mechanism that involves a catalytic triad consisting of a serine nucleophile that is activated by a proton relay involving an acidic residue (e.g. aspartate or glutamate) and a basic residue (usually histidine). GO:0005886 The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.

Target profile

Computed evidence for target prioritization.

Human off-target: No hit
Human identity (%): 0.0
Gut microbiome off-target: hit
Essential (DEG): Y
DEG identity (%): 90.432
DEG E-value: 0.0
Localization: CytoplasmicMembrane
ColabFold pLDDT: 91.26

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 0.733

Structure A0A0H3GTU0

Pocket Pocket 1

P2Rank 0.15

Structure A0A0H3GTU0

Pocket Pocket 1

ColabFold model

FPocket 0.902 · Pocket 8

P2Rank 0.126 · Pocket 1

Core conservation Conserved core gene

Roary core

CoreCruncher core

Gut microbiome 125 / 4744 genomes with a hit

Normalized 0.026

Sequence

Primary amino-acid sequence viewer.

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 7 GO

Enzyme Commission (EC)

3.4.21.89

Gene Ontology (GO)

GO:0016020 A lipid bilayer along with all the proteins and protein complexes embedded in it and attached to it.
GO:0006508 The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.
GO:0006465 OBSOLETE. The proteolytic removal of a signal peptide from a protein during or after transport to a specific location in the cell.
GO:0008236 Catalysis of the hydrolysis of peptide bonds in a polypeptide chain by a catalytic mechanism that involves a catalytic triad consisting of a serine nucleophile that is activated by a proton relay involving an acidic residue (e.g. aspartate or glutamate) and a basic residue (usually histidine).
GO:0004252 Catalysis of the hydrolysis of internal, alpha-peptide bonds in a polypeptide chain by a catalytic mechanism that involves a catalytic triad consisting of a serine nucleophile that is activated by a proton relay involving an acidic residue (e.g. aspartate or glutamate) and a basic residue (usually histidine).
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:0009003 An endopeptidase that cleaves a hydrophobic, N-terminal signal or leader sequences from mitochondrial, secreted and periplasmic proteins.

Sequence Features

Domain/signature hits from InterPro and related databases.

34 records

Show feature table

Start	End	DB	Term	Name
269	282	ProSitePatterns	PS00761	Signal peptidases I signature 3.
269	282	InterPro	IPR019758	Peptidase S26A, signal peptidase I, conserved site
76	320	Gene3D	G3DSA:2.10.109.10	Umud Fragment, subunit A
78	323	SUPERFAMILY	SSF51306	LexA/Signal peptidase
78	323	InterPro	IPR036286	LexA/Signal peptidase-like superfamily
146	158	ProSitePatterns	PS00760	Signal peptidases I lysine active site.
146	158	InterPro	IPR019757	Peptidase S26A, signal peptidase I, lysine active site
89	96	ProSitePatterns	PS00501	Signal peptidases I serine active site.
89	96	InterPro	IPR019756	Peptidase S26A, signal peptidase I, serine active site
60	82	TMHMM	TMhelix	Region of a membrane-bound protein predicted to be embedded in the membrane.
5	16	Phobius	SIGNAL_PEPTIDE_H_REGION	Hydrophobic region of a signal peptide.
155	263	Gene3D	G3DSA:2.170.230.10	-
155	263	InterPro	IPR019766	Signal peptidase I, all-beta subdomain
144	156	PRINTS	PR00727	Bacterial leader peptidase 1 (S26A) family signature
144	156	InterPro	IPR000223	Peptidase S26A, signal peptidase I
80	96	PRINTS	PR00727	Bacterial leader peptidase 1 (S26A) family signature
80	96	InterPro	IPR000223	Peptidase S26A, signal peptidase I
264	283	PRINTS	PR00727	Bacterial leader peptidase 1 (S26A) family signature
264	283	InterPro	IPR000223	Peptidase S26A, signal peptidase I
5	22	TMHMM	TMhelix	Region of a membrane-bound protein predicted to be embedded in the membrane.
62	306	PANTHER	PTHR43390	SIGNAL PEPTIDASE I
62	306	InterPro	IPR000223	Peptidase S26A, signal peptidase I
1	4	Phobius	SIGNAL_PEPTIDE_N_REGION	N-terminal region of a signal peptide.
83	297	CDD	cd06530	S26_SPase_I
83	297	InterPro	IPR019533	Peptidase S26
22	324	Phobius	NON_CYTOPLASMIC_DOMAIN	Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
262	304	NCBIfam	TIGR02227	signal peptidase I
262	304	InterPro	IPR000223	Peptidase S26A, signal peptidase I
66	159	NCBIfam	TIGR02227	signal peptidase I
66	159	InterPro	IPR000223	Peptidase S26A, signal peptidase I
60	302	Pfam	PF10502	Signal peptidase, peptidase S26
60	302	InterPro	IPR019533	Peptidase S26
17	21	Phobius	SIGNAL_PEPTIDE_C_REGION	C-terminal region of a signal peptide.
1	21	Phobius	SIGNAL_PEPTIDE	Signal peptide region

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_A0A0H3GTU0	AlphaFold	—	—	full sequence	—	Viewing
ColabFold VK055_4608	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
1				0.733
4				0.413

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				2.16	0.051
2				1.34	0.015

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				0.902
22				0.636

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	2.04	0.045
2	1.46	0.02
3	1.42	0.018

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.

29 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
CZD	6B88	P00803	892.1 Da LogP 2.05 TPSA 282.9	3 viol.	✓ Clean	`[H]/N=C\CNC(=O)[C@@H]1Cc2ccc(c(c2)-c3cc(ccc3OCC…`

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).

Ligand	UniProt (homolog)	pchembl	MW · LogP · TPSA	Lipinski	PAINS	SMILES
CHEMBL5410707	P00803	9.36	890.1 Da LogP 1.92 TPSA 282.8	3 viol.	✓ Clean	`Cc1nc(-c2ccc(C(C)(C)C)cc2)ncc1C(=O)N[C@@H](CCN)…`
CHEMBL3947604	P00803	8.22	765.7 Da LogP -0.49 TPSA 266.5	2 viol.	✓ Clean	`CCCCCCc1ccc(-c2ccc(C(=O)N3CC(CN)C[C@H]3C(=O)N[C…`
CHEMBL4284736	P00803	8.22	765.7 Da LogP -0.49 TPSA 266.5	2 viol.	✓ Clean	`CCCCCCc1ccc(-c2ccc(C(=O)N3CC(CN)C[C@H]3C(=O)N[C…`
CHEMBL3922978	P00803	7.92	870.9 Da LogP 3.58 TPSA 218.5	2 viol.	✓ Clean	`CCCCCCc1ccc(-c2ccc(C(=O)N3CCC[C@H]3C(=O)N[C@H](…`
CHEMBL4283840	P00803	7.77	887.9 Da LogP 2.82 TPSA 253.3	2 viol.	✓ Clean	`CCCCCCc1ccc(-c2ccc(C(=O)N[C@@H](CCCN)C(=O)N[C@H…`
CHEMBL3934222	P00803	7.75	899.9 Da LogP 2.77 TPSA 244.5	2 viol.	✓ Clean	`CCCCCCc1ccc(-c2ccc(C(=O)N3CC(CN)C[C@H]3C(=O)N[C…`
CHEMBL4283678	P00803	7.54	925.9 Da LogP 1.39 TPSA 278.8	3 viol.	✓ Clean	`CCCCCCc1ccc(-c2nc3cc(C(=O)N[C@@H](CCCN)C(=O)N[C…`
CHEMBL1784531	P00803	7.41	881.1 Da LogP 3.82 TPSA 255.0	2 viol.	✓ Clean	`CCCCCCCCCCCCCCCC(=O)N(C)[C@H](CO)C(=O)N[C@H](C)…`
CHEMBL4282733	P00803	7.39	926.9 Da LogP 0.56 TPSA 280.0	3 viol.	✓ Clean	`CCCCCCc1ccc(-c2ccc(C(=O)N[C@@H](CCCNC(=N)N)C(=O…`
CHEMBL4291540	P00803	7.39	834.8 Da LogP -0.56 TPSA 263.0	3 viol.	✓ Clean	`CCCCCCC#Cc1cncc(C(=O)N[C@@H](CCCN)C(=O)N[C@H](C…`
CHEMBL4291025	P00803	7.38	856.8 Da LogP 0.26 TPSA 244.2	3 viol.	✓ Clean	`CCCCc1ccc(-c2ccc(C(=O)N[C@@H](CCCN)C(=O)N[C@H](…`
CHEMBL3957297	P00803	7.32	760.8 Da LogP 1.62 TPSA 218.5	2 viol.	✓ Clean	`CCCCCCCCCC(=O)N1CCC[C@H]1C(=O)N[C@H](C(=O)N[C@@…`
CHEMBL4294422	P00803	7.28	753.7 Da LogP -0.44 TPSA 275.3	2 viol.	✓ Clean	`CCCCCCc1ccc(-c2ccc(C(=O)N[C@@H](CCCN)C(=O)N[C@H…`
CHEMBL4292925	P00803	7.14	801.7 Da LogP -0.61 TPSA 250.1	3 viol.	✓ Clean	`C[C@@H]1NC(=O)[C@@H](NC(=O)[C@H](C)NC(=O)[C@@H]…`
CHEMBL4287199	P00803	7.01	898.9 Da LogP 1.38 TPSA 235.4	3 viol.	✓ Clean	`CCCCCCc1ccc(-c2ccc(C(=O)N[C@@H](CCCN)C(=O)N(C)[…`
CHEMBL4279276	P00803	6.98	884.9 Da LogP 1.04 TPSA 244.2	3 viol.	✓ Clean	`CCCCCCc1ccc(-c2ccc(C(=O)N[C@@H](CCCN)C(=O)N[C@H…`
CHEMBL4280386	P00803	6.98	870.9 Da LogP 0.65 TPSA 244.2	3 viol.	✓ Clean	`CCCCCCc1ccc(-c2ccc(C(=O)N[C@@H](CCCN)C(=O)N[C@H…`
CHEMBL4290610	P00803	6.97	907.9 Da LogP 1.27 TPSA 246.8	3 viol.	✓ Clean	`CCCCCCc1ccc(-c2ccc(C(=O)N[C@@H](Cc3cnc[nH]3)C(=…`
CHEMBL3924425	P00803	6.96	859.9 Da LogP 2.90 TPSA 236.2	2 viol.	✓ Clean	`CCCCc1ccc(-c2ccc(C(=O)N[C@@H](CCN)C(=O)N[C@H](C…`
CHEMBL4282334	P00803	6.76	885.9 Da LogP 1.51 TPSA 250.1	3 viol.	✓ Clean	`CCCCCCc1ccc(-c2ccc(C(=O)N[C@@H](CCCN)C(=O)N[C@H…`
CHEMBL555725	P00803	6.75	215.2 Da LogP -0.18 TPSA 77.8	✓ Ro5	✓ Clean	`C[C@@H](O)[C@H]1C(=O)N2C(C(=O)O)=CS[C@@H]12`
CHEMBL4281328	P00803	6.65	924.9 Da LogP 1.99 TPSA 265.9	3 viol.	✓ Clean	`CCCCCCc1ccc(-c2c[nH]c3ccc(C(=O)N[C@@H](CCCN)C(=…`
CHEMBL3895001	P00803	6.64	736.7 Da LogP 0.33 TPSA 240.5	2 viol.	✓ Clean	`CCCCCCc1ccc(-c2ccc(C(=O)N3CCC[C@H]3C(=O)N[C@H](…`
CHEMBL4291944	P00803	6.64	825.7 Da LogP -0.87 TPSA 250.1	3 viol.	✓ Clean	`C[C@@H]1NC(=O)[C@@H](NC(=O)[C@H](C)NC(=O)[C@@H]…`
CHEMBL4280228	P00803	6.30	902.9 Da LogP -0.00 TPSA 272.1	3 viol.	✓ Clean	`CCCCCCc1ccc(-n2cc(C(=O)N[C@@H](CCCN)C(=O)N[C@H]…`
CHEMBL141679	P00803	6.07	297.3 Da LogP 1.04 TPSA 72.9	✓ Ro5	✓ Clean	`C=CCOC(=O)C1=CS[C@H]2[C@@H]([C@@H](C)OC(C)=O)C(…`
CHEMBL138375	P00803	6.04	255.3 Da LogP 0.47 TPSA 66.8	✓ Ro5	✓ Clean	`C=CCOC(=O)C1=CS[C@H]2[C@@H]([C@@H](C)O)C(=O)N12`
CHEMBL1933111	Q9M9Z2	—	1581.8 Da LogP 6.42 TPSA 421.5	4 viol.	✓ Clean	`CCOP(=O)(CCOCCOCCOCCOC(=O)NCc1cn(CCCCCNC(=O)CCC…`

Proposed virtual-screening candidates from ZINC. Score = Tanimoto similarity to a known binder (0–1; higher = more similar).

No virtual-screening candidates for this protein.

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.