Protein profile

KP13_04000

Protease degS

Genome: KpKP13

Gene: degS AHE42448.1 Structure source: AlphaFold + ColabFold UniProt A0A0H3GY66

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Amino acids 352

Annotations 7

Features 44

PDB binders 3

Druggability 0.322

Overview

Basic information about this protein and its source genome.

Accession: KP13_04000
Assembly: Klebsiella pneumoniae subsp. pneumoniae Kp13, complete sequence
Gene: degS AHE42448.1
Status: annotated
Amino acids: 352
Structure source: AlphaFold + ColabFold

3.4.21.107

GO:0006508 The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds. GO:0005515 Binding to a protein. 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: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:0005886 The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins. GO:0006515 The chemical reactions and pathways resulting in the breakdown of misfolded or attenuated proteins.

Target profile

Computed evidence for target prioritization.

Human off-target: hit
Human identity (%): 36.875
Human E-value: 1.45e-18
Gut microbiome off-target: hit
Essential (DEG): Y
DEG identity (%): 86.08
DEG E-value: 0.0
Localization: Unknown
ColabFold pLDDT: 86.62

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 0.322

Structure A0A0H3GY66

Pocket Pocket 2

P2Rank 0.169

Structure A0A0H3GY66

Pocket Pocket 1

ColabFold model

FPocket 0.427 · Pocket 2

P2Rank 0.12 · Pocket 1

Core conservation Conserved core gene

Roary core

CoreCruncher core

Gut microbiome 142 / 4744 genomes with a hit

Normalized 0.03

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)

3.4.21.107

Gene Ontology (GO)

GO:0006508 The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.
GO:0005515 Binding to a protein.
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: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:0005886 The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.
GO:0006515 The chemical reactions and pathways resulting in the breakdown of misfolded or attenuated proteins.

Sequence Features

Domain/signature hits from InterPro and related databases.

44 records

Show feature table

Start	End	DB	Term	Name
1	31	SignalP_GRAM_POSITIVE	SignalP-TM	SignalP-TM
4	349	NCBIfam	TIGR02038	outer membrane-stress sensor serine endopeptidase DegS
4	349	InterPro	IPR011783	Peptidase S1C, DegS
86	98	PRINTS	PR00834	HtrA/DegQ protease family signature
86	98	InterPro	IPR001940	Peptidase S1C
107	127	PRINTS	PR00834	HtrA/DegQ protease family signature
107	127	InterPro	IPR001940	Peptidase S1C
148	172	PRINTS	PR00834	HtrA/DegQ protease family signature
148	172	InterPro	IPR001940	Peptidase S1C
294	306	PRINTS	PR00834	HtrA/DegQ protease family signature
294	306	InterPro	IPR001940	Peptidase S1C
205	222	PRINTS	PR00834	HtrA/DegQ protease family signature
205	222	InterPro	IPR001940	Peptidase S1C
183	200	PRINTS	PR00834	HtrA/DegQ protease family signature
183	200	InterPro	IPR001940	Peptidase S1C
255	351	Gene3D	G3DSA:2.30.42.10	-
255	351	InterPro	IPR036034	PDZ superfamily
28	352	Phobius	NON_CYTOPLASMIC_DOMAIN	Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
5	24	TMHMM	TMhelix	Region of a membrane-bound protein predicted to be embedded in the membrane.
254	336	SMART	SM00228	pdz_new
254	336	InterPro	IPR001478	PDZ domain
139	253	FunFam	G3DSA:2.40.10.10:FF:000001	Periplasmic serine protease DegS
9	22	Phobius	SIGNAL_PEPTIDE_H_REGION	Hydrophobic region of a signal peptide.
139	254	Gene3D	G3DSA:2.40.10.10	-
139	254	InterPro	IPR043504	Peptidase S1, PA clan, chymotrypsin-like fold
237	343	SUPERFAMILY	SSF50156	PDZ domain-like
237	343	InterPro	IPR036034	PDZ superfamily
1	8	Phobius	SIGNAL_PEPTIDE_N_REGION	N-terminal region of a signal peptide.
254	344	Pfam	PF13180	PDZ domain
254	344	InterPro	IPR001478	PDZ domain
254	341	CDD	cd00987	PDZ_serine_protease
185	347	Pfam	PF02163	Peptidase family M50
185	347	InterPro	IPR008915	Peptidase M50
28	138	FunFam	G3DSA:2.40.10.10:FF:000009	Serine endoprotease DegS, periplasmic
41	347	PANTHER	PTHR22939	SERINE PROTEASE FAMILY S1C HTRA-RELATED
44	251	SUPERFAMILY	SSF50494	Trypsin-like serine proteases
44	251	InterPro	IPR009003	Peptidase S1, PA clan
28	138	Gene3D	G3DSA:2.40.10.10	-
28	138	InterPro	IPR043504	Peptidase S1, PA clan, chymotrypsin-like fold
23	27	Phobius	SIGNAL_PEPTIDE_C_REGION	C-terminal region of a signal peptide.
245	337	ProSiteProfiles	PS50106	PDZ domain profile.
245	337	InterPro	IPR001478	PDZ domain
1	27	Phobius	SIGNAL_PEPTIDE	Signal peptide region
77	212	Pfam	PF13365	Trypsin-like peptidase domain

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_A0A0H3GY66	AlphaFold	—	—	full sequence	—	Viewing
ColabFold KP13_04000	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
2				0.322
3				0.219

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	2.65	0.078
2	2.39	0.064
3	2.31	0.059

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
2				0.427

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				2.34	0.061
2				1.91	0.039

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.

53 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
CXS	5JD8	A0A5P8YL96	221.3 Da LogP 1.19 TPSA 66.4	✓ Ro5	✓ Clean	`C1CCC(CC1)NCCCS(=O)(=O)O`
DFP	3MH5	P0C0V0	166.2 Da LogP 2.23 TPSA 35.5	✓ Ro5	✓ Clean	`CC(C)OP(=O)OC(C)C`
PMS	6IEO	O06291	172.2 Da LogP 1.07 TPSA 54.4	✓ Ro5	✓ Clean	`c1ccc(cc1)CS(=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
ZINC2004372	1.000	221.3 Da LogP 1.19 TPSA 66.4	✓ Ro5	✓ Clean	`O=S(=O)(O)CCCNC1CCCCC1`
ZINC38364153	0.926	235.3 Da LogP 1.58 TPSA 66.4	✓ Ro5	✓ Clean	`O=S(=O)(O)CCCCNC1CCCCC1`
ZINC1710230	0.786	207.3 Da LogP 0.80 TPSA 66.4	✓ Ro5	✓ Clean	`O=S(=O)(O)CCNC1CCCCC1`
ZINC1764974	0.750	266.3 Da LogP 0.46 TPSA 108.7	✓ Ro5	✓ Clean	`O=S(=O)(O)Cc1ccc(CS(=O)(=O)O)cc1`
ZINC389634	0.714	246.3 Da LogP 2.80 TPSA 34.1	✓ Ro5	✓ Clean	`O=S(=O)(Cc1ccccc1)Cc1ccccc1`
ZINC5188799	0.630	280.5 Da LogP 4.39 TPSA 24.1	✓ Ro5	✓ Clean	`C(CCCNC1CCCCC1)CCNC1CCCCC1`
ZINC34080186	0.609	266.3 Da LogP 0.46 TPSA 108.7	✓ Ro5	✓ Clean	`O=S(=O)(O)Cc1ccccc1CS(=O)(=O)O`
ZINC32210235	0.600	251.1 Da LogP 1.84 TPSA 54.4	✓ Ro5	✓ Clean	`O=S(=O)(O)Cc1ccc(Br)cc1`
ZINC1679108	0.583	324.4 Da LogP 2.17 TPSA 68.3	✓ Ro5	✓ Clean	`O=S(=O)(Cc1ccccc1)CS(=O)(=O)Cc1ccccc1`
ZINC163130	0.560	232.3 Da LogP 2.66 TPSA 34.1	✓ Ro5	✓ Clean	`O=S(=O)(Cc1ccccc1)c1ccccc1`
ZINC196676626	0.560	340.4 Da LogP 1.14 TPSA 92.3	✓ Ro5	✓ Clean	`O=S(=O)(Cc1ccccc1)NNS(=O)(=O)Cc1ccccc1`
ZINC399776	0.560	336.4 Da LogP 2.69 TPSA 68.3	✓ Ro5	✓ Clean	`O=S(=O)(/C=C/S(=O)(=O)Cc1ccccc1)Cc1ccccc1`
ZINC145170179	0.556	250.3 Da LogP 0.48 TPSA 88.5	✓ Ro5	✓ Clean	`CS(=O)(=O)c1ccc(CS(=O)(=O)O)cc1`
ZINC1713408	0.556	214.2 Da LogP 0.69 TPSA 71.4	✓ Ro5	✓ Clean	`O=C(O)CS(=O)(=O)Cc1ccccc1`
ZINC255190110	0.556	386.5 Da LogP 3.63 TPSA 68.3	✓ Ro5	✓ Clean	`O=S(=O)(Cc1ccccc1)c1cccc(S(=O)(=O)Cc2ccccc2)c1`
ZINC26478554	0.556	200.3 Da LogP 0.59 TPSA 54.4	✓ Ro5	✓ Clean	`O=S(=O)(CCO)Cc1ccccc1`
ZINC35058157	0.552	261.3 Da LogP 2.38 TPSA 60.2	✓ Ro5	✓ Clean	`Nc1cccc(CS(=O)(=O)Cc2ccccc2)c1`
ZINC14093286	0.538	368.5 Da LogP 1.23 TPSA 92.3	✓ Ro5	✓ Clean	`O=S(=O)(Cc1ccccc1)NCCNS(=O)(=O)Cc1ccccc1`
ZINC1163467	0.536	436.6 Da LogP 4.79 TPSA 68.3	✓ Ro5	✓ Clean	`O=S(=O)(Cc1ccccc1)c1cccc2c(S(=O)(=O)Cc3ccccc3)c…`
ZINC2509149	0.531	211.4 Da LogP 4.27 TPSA 12.0	✓ Ro5	✓ Clean	`CCCCCCCCNC1CCCCC1`
ZINC32929750	0.531	289.4 Da LogP 1.90 TPSA 77.2	✓ Ro5	✓ Clean	`NC(=O)c1cccc(CS(=O)(=O)Cc2ccccc2)c1`
ZINC130127586	0.529	260.4 Da LogP 1.38 TPSA 58.2	✓ Ro5	✓ Clean	`O=S(=O)(NCCNC1CCCCCC1)C1CC1`
ZINC143515753	0.519	200.3 Da LogP 1.64 TPSA 54.4	✓ Ro5	✓ Clean	`CCc1ccccc1CS(=O)(=O)O`
ZINC19367005	0.519	224.4 Da LogP 2.83 TPSA 24.1	✓ Ro5	✓ Clean	`C1CCC(NCCNC2CCCCC2)CC1`
ZINC29840	0.519	261.3 Da LogP 2.31 TPSA 46.2	✓ Ro5	✓ Clean	`O=S(=O)(Cc1ccccc1)NCc1ccccc1`
ZINC45069273	0.519	273.6 Da LogP 2.93 TPSA 34.1	✓ Ro5	✓ Clean	`O=S(=O)(Cc1ccccc1)C(Cl)(Cl)Cl`
ZINC12805654	0.517	444.6 Da LogP 2.93 TPSA 92.3	✓ Ro5	✓ Clean	`O=S(=O)(Cc1ccccc1)NCc1cccc(CNS(=O)(=O)Cc2ccccc2…`
ZINC13808031	0.517	213.3 Da LogP -0.21 TPSA 98.5	✓ Ro5	✓ Clean	`NC(N)=NS(=O)(=O)Cc1ccccc1`
ZINC1561883	0.517	229.3 Da LogP 0.19 TPSA 83.5	✓ Ro5	✓ Clean	`O=C(O)CNS(=O)(=O)Cc1ccccc1`
ZINC1641128	0.517	242.3 Da LogP 2.68 TPSA 54.4	✓ Ro5	✓ Clean	`O=S(=O)(O)CCCCCCc1ccccc1`
ZINC17021092	0.517	228.3 Da LogP 1.07 TPSA 71.4	✓ Ro5	✓ Clean	`C[C@H](C(=O)O)S(=O)(=O)Cc1ccccc1`
ZINC1704442	0.517	228.3 Da LogP 1.07 TPSA 71.4	✓ Ro5	✓ Clean	`C[C@@H](C(=O)O)S(=O)(=O)Cc1ccccc1`
ZINC1764786	0.517	217.2 Da LogP 0.98 TPSA 97.5	✓ Ro5	✓ Clean	`O=[N+]([O-])c1ccc(CS(=O)(=O)O)cc1`
ZINC3219150	0.517	263.3 Da LogP 2.41 TPSA 57.6	✓ Ro5	✓ Clean	`O=S(=O)(Cc1ccccc1)N(O)c1ccccc1`
ZINC4512996	0.517	228.3 Da LogP 1.08 TPSA 71.4	✓ Ro5	✓ Clean	`O=C(O)CCS(=O)(=O)Cc1ccccc1`
ZINC65593788	0.517	274.4 Da LogP 3.42 TPSA 34.1	✓ Ro5	✓ Clean	`Cc1cc(C)cc(CS(=O)(=O)Cc2ccccc2)c1`
ZINC78978926	0.516	266.7 Da LogP 3.31 TPSA 34.1	✓ Ro5	✓ Clean	`O=S(=O)(Cc1ccccc1)c1cccc(Cl)c1`
ZINC96191894	0.516	217.2 Da LogP 0.98 TPSA 97.5	✓ Ro5	✓ Clean	`O=[N+]([O-])c1cccc(CS(=O)(=O)O)c1`
ZINC1641137	0.500	222.3 Da LogP 2.23 TPSA 54.4	✓ Ro5	✓ Clean	`O=S(=O)(O)Cc1cccc2ccccc12`
ZINC1672446	0.500	228.3 Da LogP 1.49 TPSA 75.3	✓ Ro5	✓ Clean	`N[C@@H](CCCCNC1CCCCC1)C(=O)O`
ZINC1926248	0.500	416.5 Da LogP 3.57 TPSA 92.3	✓ Ro5	Alert	`O=S(=O)(Cc1ccccc1)Nc1ccc(NS(=O)(=O)Cc2ccccc2)cc1`
ZINC2168583	0.500	237.3 Da LogP 0.16 TPSA 86.6	✓ Ro5	✓ Clean	`O=S(=O)(O)C[C@@H](O)CNC1CCCCC1`
ZINC2168584	0.500	237.3 Da LogP 0.16 TPSA 86.6	✓ Ro5	✓ Clean	`O=S(=O)(O)C[C@H](O)CNC1CCCCC1`
ZINC236994621	0.500	290.4 Da LogP 0.85 TPSA 75.3	✓ Ro5	✓ Clean	`CCS(=O)(=O)CC(=O)NCCNC1CCCCCC1`
ZINC29852	0.500	247.3 Da LogP 2.63 TPSA 46.2	✓ Ro5	✓ Clean	`O=S(=O)(Cc1ccccc1)Nc1ccccc1`
ZINC399887	0.500	274.3 Da LogP 2.48 TPSA 51.2	✓ Ro5	✓ Clean	`O=C(CS(=O)(=O)Cc1ccccc1)c1ccccc1`
ZINC44655186	0.500	213.4 Da LogP 3.12 TPSA 21.3	✓ Ro5	✓ Clean	`COCCCCNC1CCCCCCC1`
ZINC5840523	0.500	228.3 Da LogP 1.49 TPSA 75.3	✓ Ro5	✓ Clean	`N[C@H](CCCCNC1CCCCC1)C(=O)O`
ZINC65593700	0.500	314.3 Da LogP 3.82 TPSA 34.1	✓ Ro5	✓ Clean	`O=S(=O)(Cc1ccccc1)Cc1cccc(C(F)(F)F)c1`
ZINC728426	0.500	351.5 Da LogP 4.22 TPSA 37.4	✓ Ro5	✓ Clean	`O=S(=O)(Cc1ccccc1)N(Cc1ccccc1)Cc1ccccc1`

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.