Protein profile

KP13_00308

Oligopeptidase A

Genome: KpKP13

Gene: prlC AHE42217.1 Structure source: AlphaFold + ColabFold UniProt A0A0H3GZT5

Export view

Amino acids 680

Annotations 8

Features 14

PDB binders 2

Druggability 0.84

Overview

Basic information about this protein and its source genome.

Accession: KP13_00308
Assembly: Klebsiella pneumoniae subsp. pneumoniae Kp13, complete sequence
Gene: prlC AHE42217.1
Status: annotated
Amino acids: 680
Structure source: AlphaFold + ColabFold

3.4.24.70

GO:0004222 Catalysis of the hydrolysis of internal, alpha-peptide bonds in a polypeptide chain by a mechanism in which water acts as a nucleophile, one or two metal ions hold the water molecule in place, and charged amino acid side chains are ligands for the metal ions. GO:0006508 The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds. GO:0008233 Catalysis of the hydrolysis of a peptide bond. A peptide bond is a covalent bond formed when the carbon atom from the carboxyl group of one amino acid shares electrons with the nitrogen atom from the amino group of a second amino acid. GO:0008237 Catalysis of the hydrolysis of peptide bonds by a mechanism in which water acts as a nucleophile, one or two metal ions hold the water molecule in place, and charged amino acid side chains are ligands for the metal ions. GO:0005829 The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes. GO:0046872 Binding to a metal ion.

Target profile

Computed evidence for target prioritization.

Human off-target: hit
Human identity (%): 41.436
Human E-value: 2.25e-36
Gut microbiome off-target: hit
Essential (DEG): N
DEG identity (%): 0.0
Localization: Cytoplasmic
ColabFold pLDDT: 96.65

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 0.84

Structure A0A0H3GZT5

Pocket Pocket 2

P2Rank 0.997

Structure A0A0H3GZT5

Pocket Pocket 1

ColabFold model

FPocket 0.83 · Pocket 23

P2Rank 0.997 · Pocket 1

Core conservation Conserved core gene

Roary core

CoreCruncher core

Gut microbiome 188 / 4744 genomes with a hit

Normalized 0.04

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)

3.4.24.70

Gene Ontology (GO)

GO:0004222 Catalysis of the hydrolysis of internal, alpha-peptide bonds in a polypeptide chain by a mechanism in which water acts as a nucleophile, one or two metal ions hold the water molecule in place, and charged amino acid side chains are ligands for the metal ions.
GO:0006508 The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.
GO:0008233 Catalysis of the hydrolysis of a peptide bond. A peptide bond is a covalent bond formed when the carbon atom from the carboxyl group of one amino acid shares electrons with the nitrogen atom from the amino group of a second amino acid.
GO:0008237 Catalysis of the hydrolysis of peptide bonds by a mechanism in which water acts as a nucleophile, one or two metal ions hold the water molecule in place, and charged amino acid side chains are ligands for the metal ions.
GO:0005829 The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
GO:0046872 Binding to a metal ion.
GO:0006518 The chemical reactions and pathways involving peptides, compounds of two or more amino acids where the alpha carboxyl group of one is bound to the alpha amino group of another.

Sequence Features

Domain/signature hits from InterPro and related databases.

14 records

Show feature table

Start	End	DB	Term	Name
358	508	Gene3D	G3DSA:3.40.390.10	Collagenase (Catalytic Domain)
358	508	InterPro	IPR024079	Metallopeptidase, catalytic domain superfamily
3	679	PANTHER	PTHR11804	PROTEASE M3 THIMET OLIGOPEPTIDASE-RELATED
3	679	InterPro	IPR045090	Peptidase M3A/M3B
358	508	FunFam	G3DSA:3.40.390.10:FF:000009	Oligopeptidase A
20	678	CDD	cd06456	M3A_DCP
20	678	InterPro	IPR034005	Peptidyl-dipeptidase DCP
1	677	SUPERFAMILY	SSF55486	Metalloproteases ("zincins"), catalytic domain
150	673	Gene3D	G3DSA:1.10.1370.10	Neurolysin, domain 3
150	673	InterPro	IPR024077	Neurolysin/Thimet oligopeptidase, domain 2
222	677	Pfam	PF01432	Peptidase family M3
222	677	InterPro	IPR001567	Peptidase M3A/M3B catalytic domain
35	147	Pfam	PF19310	Neurolysin/Thimet oligopeptidase, N-terminal domain
35	147	InterPro	IPR045666	Oligopeptidase A, N-terminal 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...

Legend High Medium Low

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_A0A0H3GZT5	AlphaFold	—	—	full sequence	—	Viewing
ColabFold KP13_00308	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				0.84
44				0.22

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	35.19	0.952
2	21.7	0.873
3	19.21	0.836
4	12.66	0.658
5	7.1	0.368

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
23				0.83
1				0.703
36				0.268

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	19.03	0.833
2	17.6	0.805
3	17.07	0.795
4	16.33	0.777
5	8.94	0.479

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.

57 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
0W2	4FXY	P42676	525.1 Da LogP 5.69 TPSA 64.7	2 viol.	✓ Clean	`C[C@@H](C(=O)N1CC[C@@H](N1c2ccccc2F)c3ccccc3Cl)…`
K26	5L44	A0A1L1QK30	535.5 Da LogP 1.54 TPSA 185.3	2 viol.	✓ Clean	`CC[C@H](C)[C@@H](C(=O)N[C@@H](Cc1ccc(cc1)O)C(=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).

Ligand	UniProt (homolog)	pchembl	MW · LogP · TPSA	Lipinski	PAINS	SMILES
DWT	Q9BYT8	6.97	503.5 Da LogP 5.75 TPSA 97.6	2 viol.	✓ Clean	`Cc1ccc(cc1Nc2c3cn(nc3nc(n2)c4cccnc4)C)C(=O)Nc5c…`
CHEMBL5070123	P42676	6.00	297.4 Da LogP 1.12 TPSA 99.6	✓ Ro5	✓ Clean	`N[C@H](Cc1c[nH]cn1)C(=O)NCCc1cc2ccccc2[nH]1`
CHEMBL5079973	P52888	—	297.4 Da LogP 1.12 TPSA 99.6	✓ Ro5	✓ Clean	`N[C@@H](Cc1c[nH]cn1)C(=O)NCCc1cc2ccccc2[nH]1`
CHEMBL5092803	P42676	—	294.4 Da LogP 1.75 TPSA 83.8	✓ Ro5	✓ Clean	`N[C@@H](Cc1c[nH]cn1)C(=O)NCc1cccc2ccccc12`
CHEMBL5284556	P42676	—	295.3 Da LogP 1.14 TPSA 96.7	✓ Ro5	✓ Clean	`N[C@@H](Cc1c[nH]cn1)C(=O)NCc1cccc2cccnc12`

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
ZINC4899521	0.778	203.2 Da LogP 0.52 TPSA 84.9	✓ Ro5	✓ Clean	`NC(=O)[C@H](N)Cc1c[nH]c2ccccc12`
ZINC57505	0.778	203.2 Da LogP 0.52 TPSA 84.9	✓ Ro5	✓ Clean	`NC(=O)[C@@H](N)Cc1c[nH]c2ccccc12`
ZINC2566035	0.757	218.3 Da LogP 1.51 TPSA 79.1	✓ Ro5	✓ Clean	`N[C@@H](CCc1c[nH]c2ccccc12)C(=O)O`
ZINC6864822	0.757	218.3 Da LogP 1.51 TPSA 79.1	✓ Ro5	✓ Clean	`N[C@H](CCc1c[nH]c2ccccc12)C(=O)O`
ZINC1690614	0.743	233.2 Da LogP 1.50 TPSA 90.4	✓ Ro5	✓ Clean	`O=C(O)C(Cc1c[nH]c2ccccc12)C(=O)O`
ZINC14982898	0.711	220.2 Da LogP 0.83 TPSA 99.3	✓ Ro5	✓ Clean	`N[C@@H](Cc1c[nH]c2c(O)cccc12)C(=O)O`
ZINC14982901	0.711	220.2 Da LogP 0.83 TPSA 99.3	✓ Ro5	✓ Clean	`N[C@H](Cc1c[nH]c2c(O)cccc12)C(=O)O`
ZINC35051054	0.707	294.4 Da LogP 2.78 TPSA 68.1	✓ Ro5	✓ Clean	`N[C@H](Cc1c[nH]c2ccccc12)C(=O)OCc1ccccc1`
ZINC35051056	0.707	294.4 Da LogP 2.78 TPSA 68.1	✓ Ro5	✓ Clean	`N[C@@H](Cc1c[nH]c2ccccc12)C(=O)OCc1ccccc1`
ZINC39098	0.703	205.2 Da LogP 1.16 TPSA 73.3	✓ Ro5	✓ Clean	`O=C(O)[C@@H](O)Cc1c[nH]c2ccccc12`
ZINC39099	0.703	205.2 Da LogP 1.16 TPSA 73.3	✓ Ro5	✓ Clean	`O=C(O)[C@H](O)Cc1c[nH]c2ccccc12`
ZINC83138991	0.703	268.1 Da LogP 2.56 TPSA 53.1	✓ Ro5	✓ Clean	`O=C(O)[C@@H](Br)Cc1c[nH]c2ccccc12`
ZINC52968847	0.700	232.3 Da LogP 1.60 TPSA 68.1	✓ Ro5	✓ Clean	`CCOC(=O)[C@@H](N)Cc1c[nH]c2ccccc12`
ZINC53943847	0.700	232.3 Da LogP 1.60 TPSA 68.1	✓ Ro5	✓ Clean	`CCOC(=O)[C@H](N)Cc1c[nH]c2ccccc12`
ZINC32189073	0.692	220.2 Da LogP 0.83 TPSA 99.3	✓ Ro5	✓ Clean	`N[C@H](Cc1c[nH]c2cccc(O)c12)C(=O)O`
ZINC4240327	0.692	218.3 Da LogP 1.51 TPSA 79.1	✓ Ro5	✓ Clean	`N[C@H](CC(=O)O)Cc1c[nH]c2ccccc12`
ZINC44544883	0.692	218.3 Da LogP 1.37 TPSA 79.1	✓ Ro5	✓ Clean	`NC[C@H](Cc1c[nH]c2ccccc12)C(=O)O`
ZINC44544886	0.692	218.3 Da LogP 1.37 TPSA 79.1	✓ Ro5	✓ Clean	`NC[C@@H](Cc1c[nH]c2ccccc12)C(=O)O`
ZINC4521117	0.692	218.3 Da LogP 1.51 TPSA 79.1	✓ Ro5	✓ Clean	`N[C@@H](CC(=O)O)Cc1c[nH]c2ccccc12`
ZINC5843989	0.692	220.2 Da LogP 0.83 TPSA 99.3	✓ Ro5	✓ Clean	`N[C@@H](Cc1c[nH]c2cccc(O)c12)C(=O)O`
ZINC178385	0.684	203.2 Da LogP 2.43 TPSA 53.1	✓ Ro5	✓ Clean	`C[C@@H](Cc1c[nH]c2ccccc12)C(=O)O`
ZINC178387	0.684	203.2 Da LogP 2.43 TPSA 53.1	✓ Ro5	✓ Clean	`C[C@H](Cc1c[nH]c2ccccc12)C(=O)O`
ZINC2539067	0.682	333.4 Da LogP 3.19 TPSA 94.9	✓ Ro5	Alert	`N[C@@H](Cc1c(Cc2c[nH]c3ccccc23)[nH]c2ccccc12)C(…`
ZINC114287530	0.675	330.1 Da LogP 1.73 TPSA 79.1	✓ Ro5	✓ Clean	`N[C@H](Cc1c[nH]c2ccc(I)cc12)C(=O)O`
ZINC14512177	0.675	220.2 Da LogP 0.83 TPSA 99.3	✓ Ro5	✓ Clean	`N[C@@H](Cc1c[nH]c2cc(O)ccc12)C(=O)O`
ZINC14512180	0.675	220.2 Da LogP 0.83 TPSA 99.3	✓ Ro5	✓ Clean	`N[C@H](Cc1c[nH]c2cc(O)ccc12)C(=O)O`
ZINC1691594	0.675	219.2 Da LogP 0.70 TPSA 105.1	✓ Ro5	✓ Clean	`Nc1ccc2[nH]cc(C[C@H](N)C(=O)O)c2c1`
ZINC34279958	0.675	330.1 Da LogP 1.73 TPSA 79.1	✓ Ro5	✓ Clean	`N[C@@H](Cc1c[nH]c2ccc(I)cc12)C(=O)O`
ZINC57131	0.675	283.1 Da LogP 1.88 TPSA 79.1	✓ Ro5	✓ Clean	`N[C@@H](Cc1c[nH]c2ccc(Br)cc12)C(=O)O`
ZINC57132	0.675	283.1 Da LogP 1.88 TPSA 79.1	✓ Ro5	✓ Clean	`N[C@H](Cc1c[nH]c2ccc(Br)cc12)C(=O)O`
ZINC6045354	0.675	219.2 Da LogP 0.70 TPSA 105.1	✓ Ro5	✓ Clean	`Nc1ccc2[nH]cc(C[C@@H](N)C(=O)O)c2c1`
ZINC895330	0.675	220.2 Da LogP 0.83 TPSA 99.3	✓ Ro5	✓ Clean	`N[C@@H](Cc1c[nH]c2ccc(O)cc12)C(=O)O`
ZINC895459	0.675	220.2 Da LogP 0.83 TPSA 99.3	✓ Ro5	✓ Clean	`N[C@H](Cc1c[nH]c2ccc(O)cc12)C(=O)O`
ZINC20269567	0.667	265.3 Da LogP 3.58 TPSA 53.1	✓ Ro5	✓ Clean	`O=C(O)[C@@H](Cc1c[nH]c2ccccc12)c1ccccc1`
ZINC20269568	0.667	265.3 Da LogP 3.58 TPSA 53.1	✓ Ro5	✓ Clean	`O=C(O)[C@H](Cc1c[nH]c2ccccc12)c1ccccc1`
ZINC34402729	0.667	204.2 Da LogP 1.12 TPSA 79.1	✓ Ro5	✓ Clean	`N[C@@H](Cc1cccc2[nH]ccc12)C(=O)O`
ZINC34402730	0.667	204.2 Da LogP 1.12 TPSA 79.1	✓ Ro5	✓ Clean	`N[C@H](Cc1cccc2[nH]ccc12)C(=O)O`
ZINC34751367	0.667	260.3 Da LogP 2.38 TPSA 68.1	✓ Ro5	✓ Clean	`CC(C)(C)OC(=O)[C@H](N)Cc1c[nH]c2ccccc12`
ZINC36468154	0.667	244.3 Da LogP 1.77 TPSA 68.1	✓ Ro5	✓ Clean	`C=CCOC(=O)[C@@H](N)Cc1c[nH]c2ccccc12`
ZINC59313451	0.667	260.3 Da LogP 2.38 TPSA 68.1	✓ Ro5	✓ Clean	`CC(C)(C)OC(=O)[C@@H](N)Cc1c[nH]c2ccccc12`
ZINC2516136	0.659	283.1 Da LogP 1.88 TPSA 79.1	✓ Ro5	✓ Clean	`N[C@@H](Cc1c[nH]c2cc(Br)ccc12)C(=O)O`
ZINC2572392	0.659	238.7 Da LogP 1.78 TPSA 79.1	✓ Ro5	✓ Clean	`N[C@@H](Cc1c[nH]c2ccc(Cl)cc12)C(=O)O`
ZINC391256	0.659	218.3 Da LogP 1.43 TPSA 79.1	✓ Ro5	✓ Clean	`Cc1ccc2[nH]cc(C[C@H](N)C(=O)O)c2c1`
ZINC391257	0.659	218.3 Da LogP 1.43 TPSA 79.1	✓ Ro5	✓ Clean	`Cc1ccc2[nH]cc(C[C@@H](N)C(=O)O)c2c1`
ZINC391258	0.659	218.3 Da LogP 1.43 TPSA 79.1	✓ Ro5	✓ Clean	`Cc1ccc2c(C[C@H](N)C(=O)O)c[nH]c2c1`
ZINC391781	0.659	218.3 Da LogP 1.43 TPSA 79.1	✓ Ro5	✓ Clean	`Cc1ccc2c(C[C@@H](N)C(=O)O)c[nH]c2c1`
ZINC56393	0.659	222.2 Da LogP 1.26 TPSA 79.1	✓ Ro5	✓ Clean	`N[C@@H](Cc1c[nH]c2cc(F)ccc12)C(=O)O`
ZINC57156	0.659	222.2 Da LogP 1.26 TPSA 79.1	✓ Ro5	✓ Clean	`N[C@@H](Cc1c[nH]c2ccc(F)cc12)C(=O)O`
ZINC57157	0.659	222.2 Da LogP 1.26 TPSA 79.1	✓ Ro5	✓ Clean	`N[C@H](Cc1c[nH]c2ccc(F)cc12)C(=O)O`
ZINC9915769	0.659	238.7 Da LogP 1.78 TPSA 79.1	✓ Ro5	✓ Clean	`N[C@H](Cc1c[nH]c2ccc(Cl)cc12)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.