Protein profile

KP13_02292

Protease 3

Genome: KpKP13

Gene: ptrA AHE42863.1 Structure source: AlphaFold + ColabFold UniProt A0A0H3GXU7
Amino acids 961
Annotations 5
Features 31
PDB binders 16
Druggability 0.797

Overview

Basic information about this protein and its source genome.

Accession
KP13_02292
Gene
ptrA AHE42863.1
Status
annotated
Amino acids
961
Structure source
AlphaFold + ColabFold

Target profile

Computed evidence for target prioritization.

Human off-target
hit
Human identity (%)
33.981
Human E-value
4.83e-06
Gut microbiome off-target
hit
Essential (DEG)
N
DEG identity (%)
0.0
Localization
Periplasmic
ColabFold pLDDT
93.74

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 0.797
Structure A0A0H3GXU7
Pocket Pocket 2
P2Rank 0.688
Structure A0A0H3GXU7
Pocket Pocket 1
ColabFold model
FPocket 0.204 · Pocket 6
P2Rank 0.868 · Pocket 1
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 101 / 4744 genomes with a hit
Normalized 0.021

Sequence

Primary amino-acid sequence viewer.

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 4 GO

Enzyme Commission (EC)

1

Gene Ontology (GO)

4
  • 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:0046872 Binding to a metal ion.
  • GO:0005737 The contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

Sequence Features

Domain/signature hits from InterPro and related databases.

31 records
Show feature table
Start End DB Term Name
1 23 SignalP_EUK SignalP-noTM SignalP-noTM
504 729 SUPERFAMILY SSF63411 LuxS/MPP-like metallohydrolase
504 729 InterPro IPR011249 Metalloenzyme, LuxS/M16 peptidase-like
265 502 SUPERFAMILY SSF63411 LuxS/MPP-like metallohydrolase
265 502 InterPro IPR011249 Metalloenzyme, LuxS/M16 peptidase-like
24 961 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
652 917 Gene3D G3DSA:3.30.830.10 -
272 502 Gene3D G3DSA:3.30.830.10 -
1 23 Phobius SIGNAL_PEPTIDE Signal peptide region
1 8 Phobius SIGNAL_PEPTIDE_N_REGION N-terminal region of a signal peptide.
24 260 FunFam G3DSA:3.30.830.10:FF:000012 Protease 3
504 885 Gene3D G3DSA:3.30.830.10 -
54 191 Pfam PF00675 Insulinase (Peptidase family M16)
54 191 InterPro IPR011765 Peptidase M16, N-terminal
737 957 SUPERFAMILY SSF63411 LuxS/MPP-like metallohydrolase
737 957 InterPro IPR011249 Metalloenzyme, LuxS/M16 peptidase-like
1 23 SignalP_GRAM_POSITIVE SignalP-TM SignalP-TM
681 856 Pfam PF05193 Peptidase M16 inactive domain
681 856 InterPro IPR007863 Peptidase M16, C-terminal
215 392 Pfam PF05193 Peptidase M16 inactive domain
215 392 InterPro IPR007863 Peptidase M16, C-terminal
33 262 SUPERFAMILY SSF63411 LuxS/MPP-like metallohydrolase
33 262 InterPro IPR011249 Metalloenzyme, LuxS/M16 peptidase-like
75 98 ProSitePatterns PS00143 Insulinase family, zinc-binding region signature.
75 98 InterPro IPR001431 Peptidase M16, zinc-binding site
9 18 Phobius SIGNAL_PEPTIDE_H_REGION Hydrophobic region of a signal peptide.
19 23 Phobius SIGNAL_PEPTIDE_C_REGION C-terminal region of a signal peptide.
400 673 Pfam PF16187 Middle or third domain of peptidase_M16
400 673 InterPro IPR032632 Peptidase M16, middle/third domain
24 271 Gene3D G3DSA:3.30.830.10 -
31 912 PANTHER PTHR43690 NARDILYSIN

3D Structure

Selected loaded structure. Experimental PDB entries may cover only a portion of the sequence; predicted models typically cover the full protein.

3D visualization script Full viewer

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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_A0A0H3GXU7
AlphaFold full sequence Viewing
ColabFold KP13_02292
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 0.797
70 0.505
13 0.346
3 0.278

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 5.22 0.242
2 4.44 0.188
3 4.14 0.168
4 3.32 0.117
5 3.05 0.101

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.

78 records

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.

Show only:
Ligand Source crystal UniProt (homolog) MW · LogP · TPSA Lipinski PAINS SMILES
1EF P14735 443.5 Da LogP 3.35 TPSA 109.1 ✓ Ro5 ✓ Clean Cc1ccc(cc1)C(=O)NCc2cn(nn2)[C@H](Cc3ccc4ccccc4c…
2H7 P14735 447.5 Da LogP 3.18 TPSA 109.1 ✓ Ro5 ✓ Clean c1ccc2cc(ccc2c1)C[C@H](CC(=O)NO)n3cc(nn3)CNC(=O…
2PJ P14735 398.5 Da LogP 5.36 TPSA 51.2 1 viol. ✓ Clean CC(C)(C)OC(=O)NC[C@@H](Cc1cc2ccccc2nc1)c3cc(ccc…
2Q6 P14735 734.0 Da LogP 7.55 TPSA 135.9 2 viol. ✓ Clean COC(=O)NC[C@@H](Cc1cc2ccccc2nc1)c3ccc(cc3)OCCCC…
2QW P14735 424.4 Da LogP 2.89 TPSA 84.2 ✓ Ro5 ✓ Clean Cc1ccc(cc1)NC(=O)[C@H](C2CCCCC2)NC(=O)[C@H](CC[…
2QX P14735 735.9 Da LogP 7.85 TPSA 126.6 2 viol. ✓ Clean COC(=O)NC[C@@H](Cc1cc2ccccc2nc1)c3cc(ccc3F)CCCC…
33K P14735 360.4 Da LogP 0.11 TPSA 135.6 ✓ Ro5 ✓ Clean c1ccc(cc1)CN(CC(=O)N[C@@H](Cc2cnc[nH]2)C(=O)O)C…
3M9 P14735 447.5 Da LogP 3.18 TPSA 109.1 ✓ Ro5 ✓ Clean c1ccc2cc(ccc2c1)C[C@H](CC(=O)NO)n3c(cnn3)CNC(=O…
I41 P14735 374.4 Da LogP 0.20 TPSA 124.6 ✓ Ro5 ✓ Clean COC(=O)[C@H](Cc1cnc[nH]1)NC(=O)C[N@](Cc2ccccc2)…
J18 P14735 558.7 Da LogP 5.60 TPSA 60.9 2 viol. ✓ Clean Cc1cccc(c1C)c2ccc(cc2)[C@H]3[C@@H]4CN(CCCCN4[C@…
J22 P14735 494.7 Da LogP 3.32 TPSA 78.7 ✓ Ro5 ✓ Clean Cc1cccc(c1C)c2ccc(cc2)[C@H]3[C@@H]4CN(CCCCN4[C@…
MGH P14735 416.4 Da LogP 0.16 TPSA 141.7 ✓ Ro5 ✓ Clean COC(=O)[C@@H](Cc1c[nH]cn1)NC(=O)CN(CC(=O)O)C(=O…
MGJ P14735 401.5 Da LogP 0.20 TPSA 127.4 ✓ Ro5 ✓ Clean CNC(=O)[C@H](Cc1c[nH]cn1)NC(=O)C[N@](CCCc2ccccc…
MGK P14735 402.5 Da LogP 0.63 TPSA 124.6 ✓ Ro5 ✓ Clean COC(=O)[C@H](Cc1cnc[nH]1)NC(=O)C[N@](CCCc2ccccc…
MGW P14735 388.4 Da LogP 0.24 TPSA 124.6 ✓ Ro5 ✓ Clean COC(=O)[C@H](Cc1cnc[nH]1)NC(=O)C[N@@](CCc2ccccc…
QIX P14735 542.6 Da LogP -1.64 TPSA 241.6 2 viol. ✓ Clean [H]/N=C(/N)\NCCC[C@@H](C(=O)NCC(=O)NCC(=O)N)NC(…

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.