Protein profile

KP13_01817

Periplasmic serine endoprotease DegP

Genome: KpKP13

Gene: degP AHE46257.1 Structure source: AlphaFold + ColabFold UniProt A0A0H3GJM8

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Amino acids 480

Annotations 4

Features 58

PDB binders 3

Druggability 0.346

Overview

Basic information about this protein and its source genome.

Accession: KP13_01817
Assembly: Klebsiella pneumoniae subsp. pneumoniae Kp13, complete sequence
Gene: degP AHE46257.1
Status: annotated
Amino acids: 480
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).

Target profile

Computed evidence for target prioritization.

Human off-target: hit
Human identity (%): 47.015
Human E-value: 6.61e-22
Gut microbiome off-target: hit
Essential (DEG): Y
DEG identity (%): 56.042
DEG E-value: 0.0
Localization: Periplasmic
ColabFold pLDDT: 82.15

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 0.346

Structure A0A0H3GJM8

Pocket Pocket 21

P2Rank 0.431

Structure A0A0H3GJM8

Pocket Pocket 1

ColabFold model

FPocket 0.265 · Pocket 22

P2Rank 0.336 · Pocket 1

Core conservation Conserved core gene

Roary core

CoreCruncher core

Gut microbiome 162 / 4744 genomes with a hit

Normalized 0.034

Sequence

Primary amino-acid sequence viewer.

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 3 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).

Sequence Features

Domain/signature hits from InterPro and related databases.

58 records

Show feature table

Start	End	DB	Term	Name
279	403	Pfam	PF02163	Peptidase family M50
279	403	InterPro	IPR008915	Peptidase M50
415	470	Pfam	PF02163	Peptidase family M50
415	470	InterPro	IPR008915	Peptidase M50
183	294	FunFam	G3DSA:2.40.10.10:FF:000001	Periplasmic serine protease DegS
295	377	SMART	SM00228	pdz_new
295	377	InterPro	IPR001478	PDZ domain
402	472	SMART	SM00228	pdz_new
402	472	InterPro	IPR001478	PDZ domain
23	29	Phobius	SIGNAL_PEPTIDE_C_REGION	C-terminal region of a signal peptide.
286	377	ProSiteProfiles	PS50106	PDZ domain profile.
286	377	InterPro	IPR001478	PDZ domain
277	386	SUPERFAMILY	SSF50156	PDZ domain-like
277	386	InterPro	IPR036034	PDZ superfamily
30	480	Phobius	NON_CYTOPLASMIC_DOMAIN	Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
42	289	Gene3D	G3DSA:2.40.10.120	-
1	11	Phobius	SIGNAL_PEPTIDE_N_REGION	N-terminal region of a signal peptide.
395	480	FunFam	G3DSA:2.30.42.10:FF:000050	Periplasmic serine endoprotease DegP-like
44	478	NCBIfam	TIGR02037	Do family serine endopeptidase
44	478	InterPro	IPR011782	Peptidase S1C, Do
1	29	Phobius	SIGNAL_PEPTIDE	Signal peptide region
42	289	FunFam	G3DSA:2.40.10.120:FF:000001	Periplasmic serine endoprotease DegP-like
414	475	PANTHER	PTHR22939	SERINE PROTEASE FAMILY S1C HTRA-RELATED
303	386	Pfam	PF13180	PDZ domain
303	386	InterPro	IPR001478	PDZ domain
1	29	SignalP_GRAM_POSITIVE	SignalP-TM	SignalP-TM
394	480	Gene3D	G3DSA:2.30.42.10	-
394	480	InterPro	IPR036034	PDZ superfamily
192	216	PRINTS	PR00834	HtrA/DegQ protease family signature
192	216	InterPro	IPR001940	Peptidase S1C
249	266	PRINTS	PR00834	HtrA/DegQ protease family signature
249	266	InterPro	IPR001940	Peptidase S1C
227	244	PRINTS	PR00834	HtrA/DegQ protease family signature
227	244	InterPro	IPR001940	Peptidase S1C
151	171	PRINTS	PR00834	HtrA/DegQ protease family signature
151	171	InterPro	IPR001940	Peptidase S1C
335	347	PRINTS	PR00834	HtrA/DegQ protease family signature
335	347	InterPro	IPR001940	Peptidase S1C
130	142	PRINTS	PR00834	HtrA/DegQ protease family signature
130	142	InterPro	IPR001940	Peptidase S1C
91	111	MobiDBLite	mobidb-lite	consensus disorder prediction
1	29	SignalP_EUK	SignalP-noTM	SignalP-noTM
297	384	CDD	cd00987	PDZ_serine_protease
12	22	Phobius	SIGNAL_PEPTIDE_H_REGION	Hydrophobic region of a signal peptide.
39	304	SUPERFAMILY	SSF50494	Trypsin-like serine proteases
39	304	InterPro	IPR009003	Peptidase S1, PA clan
293	393	Gene3D	G3DSA:2.30.42.10	-
293	393	InterPro	IPR036034	PDZ superfamily
120	256	Pfam	PF13365	Trypsin-like peptidase domain
406	477	CDD	cd00987	PDZ_serine_protease
91	112	MobiDBLite	mobidb-lite	consensus disorder prediction
293	394	FunFam	G3DSA:2.30.42.10:FF:000037	Periplasmic serine endoprotease DegP-like
397	469	Pfam	PF00595	PDZ domain
397	469	InterPro	IPR001478	PDZ domain
405	476	SUPERFAMILY	SSF50156	PDZ domain-like
405	476	InterPro	IPR036034	PDZ superfamily
383	472	ProSiteProfiles	PS50106	PDZ domain profile.
383	472	InterPro	IPR001478	PDZ 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_A0A0H3GJM8	AlphaFold	—	—	full sequence	—	Viewing
ColabFold KP13_01817	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
21				0.346

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	2.99	0.097
2	2.69	0.08
3	1.34	0.015
4	1.28	0.013
5	0.94	0.004

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
22				0.265
1				0.224

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				2.28	0.057
2				1.51	0.022

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.