Protein profile

KP13_01146

Peptidyl-dipeptidase dcp

Genome: KpKP13

Gene: dcp AHE44728.1 Structure source: AlphaFold + ColabFold UniProt A0A0H3GT32

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Amino acids 681

Annotations 9

Features 14

PDB binders 2

Druggability 0.336

Overview

Basic information about this protein and its source genome.

Accession: KP13_01146
Assembly: Klebsiella pneumoniae subsp. pneumoniae Kp13, complete sequence
Gene: dcp AHE44728.1
Status: annotated
Amino acids: 681
Structure source: AlphaFold + ColabFold

3.4.15.5

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:0004180 Catalysis of the hydrolysis of a single C-terminal amino acid residue from a polypeptide chain.

Target profile

Computed evidence for target prioritization.

Human off-target: hit
Human identity (%): 34.682
Human E-value: 4.4499999999999995e-24
Gut microbiome off-target: hit
Essential (DEG): N
DEG identity (%): 0.0
Localization: Cytoplasmic
ColabFold pLDDT: 95.5

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 0.336

Structure A0A0H3GT32

Pocket Pocket 2

P2Rank 0.997

Structure A0A0H3GT32

Pocket Pocket 1

ColabFold model

FPocket 0.511 · Pocket 1

P2Rank 0.427 · Pocket 1

Core conservation Conserved core gene

Roary core

CoreCruncher core

Gut microbiome 86 / 4744 genomes with a hit

Normalized 0.018

Sequence

Primary amino-acid sequence viewer.

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 8 GO

Enzyme Commission (EC)

3.4.15.5

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:0004180 Catalysis of the hydrolysis of a single C-terminal amino acid residue from a polypeptide chain.
GO:0046872 Binding to a metal ion.
GO:0008241 Catalysis of the release of C-terminal dipeptides from a polypeptide chain.

Sequence Features

Domain/signature hits from InterPro and related databases.

14 records

Show feature table

Start	End	DB	Term	Name
3	680	PANTHER	PTHR43660	DIPEPTIDYL CARBOXYPEPTIDASE
3	680	InterPro	IPR045090	Peptidase M3A/M3B
157	674	Gene3D	G3DSA:1.10.1370.10	Neurolysin, domain 3
157	674	InterPro	IPR024077	Neurolysin/Thimet oligopeptidase, domain 2
338	597	FunFam	G3DSA:1.10.1370.40:FF:000001	Dipeptidyl carboxypeptidase II
232	678	Pfam	PF01432	Peptidase family M3
232	678	InterPro	IPR001567	Peptidase M3A/M3B catalytic domain
12	678	SUPERFAMILY	SSF55486	Metalloproteases ("zincins"), catalytic domain
2	155	Gene3D	G3DSA:1.10.1370.40	-
26	679	CDD	cd06456	M3A_DCP
26	679	InterPro	IPR034005	Peptidyl-dipeptidase DCP
361	508	FunFam	G3DSA:3.40.390.10:FF:000009	Oligopeptidase A
361	508	Gene3D	G3DSA:3.40.390.10	Collagenase (Catalytic Domain)
361	508	InterPro	IPR024079	Metallopeptidase, catalytic domain superfamily

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_A0A0H3GT32	AlphaFold	—	—	full sequence	—	Viewing
ColabFold KP13_01146	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				0.336

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	65.51	0.99
2	10.07	0.542
3	2.8	0.087
4	2.79	0.086
5	2.59	0.074

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				0.511
25				0.47
30				0.26

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	5.99	0.295
2	3.02	0.099
3	2.95	0.095
4	2.91	0.093
5	2.72	0.082

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.