Overview
Basic information about this protein and its source genome.
- Accession
- KP13_31631
- Gene
- AHE46191.1 pepD
- Status
- annotated
- Amino acids
- 485
- Structure source
- AlphaFold + ColabFold
Target profile
Computed evidence for target prioritization.
- Human off-target
- No hit
- Human identity (%)
- 0.0
- Gut microbiome off-target
- hit
- Essential (DEG)
- Y
- DEG identity (%)
- 55.031
- DEG E-value
- 0.0
- Localization
- Cytoplasmic
- ColabFold pLDDT
- 96.26
Selected Druggability evidence
AlphaFold / UniProt modelSelected 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.
Sequence
Primary amino-acid sequence viewer.
Functional Annotations
Enzyme classification and Gene Ontology terms linked to this protein.
Enzyme Commission (EC)
1Gene Ontology (GO)
5- GO:0006508 The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.
- GO:0016787 Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc.
- 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:0070573 Catalysis of the hydrolysis of a dipeptide 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.
Sequence Features
Domain/signature hits from InterPro and related databases.
Show feature table
| Start | End | DB | Term | Name |
|---|---|---|---|---|
| 1 | 484 | PANTHER | PTHR43501 | CYTOSOL NON-SPECIFIC DIPEPTIDASE |
| 1 | 484 | InterPro | IPR001160 | Peptidase M20C, Xaa-His dipeptidase |
| 368 | 485 | Gene3D | G3DSA:3.40.630.10 | Zn peptidases |
| 1 | 233 | Gene3D | G3DSA:3.40.630.10 | Zn peptidases |
| 1 | 485 | PIRSF | PIRSF016599 | Xaa-His_dipept |
| 1 | 485 | InterPro | IPR001160 | Peptidase M20C, Xaa-His dipeptidase |
| 8 | 482 | NCBIfam | TIGR01893 | beta-Ala-His dipeptidase |
| 8 | 482 | InterPro | IPR001160 | Peptidase M20C, Xaa-His dipeptidase |
| 9 | 482 | CDD | cd03890 | M20_pepD |
| 9 | 482 | InterPro | IPR001160 | Peptidase M20C, Xaa-His dipeptidase |
| 203 | 293 | Pfam | PF07687 | Peptidase dimerisation domain |
| 203 | 293 | InterPro | IPR011650 | Peptidase M20, dimerisation domain |
| 428 | 444 | PRINTS | PR00934 | X-His dipeptidase (M25) signature |
| 428 | 444 | InterPro | IPR001160 | Peptidase M20C, Xaa-His dipeptidase |
| 80 | 99 | PRINTS | PR00934 | X-His dipeptidase (M25) signature |
| 80 | 99 | InterPro | IPR001160 | Peptidase M20C, Xaa-His dipeptidase |
| 450 | 472 | PRINTS | PR00934 | X-His dipeptidase (M25) signature |
| 450 | 472 | InterPro | IPR001160 | Peptidase M20C, Xaa-His dipeptidase |
| 363 | 381 | PRINTS | PR00934 | X-His dipeptidase (M25) signature |
| 363 | 381 | InterPro | IPR001160 | Peptidase M20C, Xaa-His dipeptidase |
| 206 | 223 | PRINTS | PR00934 | X-His dipeptidase (M25) signature |
| 206 | 223 | InterPro | IPR001160 | Peptidase M20C, Xaa-His dipeptidase |
| 101 | 119 | PRINTS | PR00934 | X-His dipeptidase (M25) signature |
| 101 | 119 | InterPro | IPR001160 | Peptidase M20C, Xaa-His dipeptidase |
| 135 | 152 | PRINTS | PR00934 | X-His dipeptidase (M25) signature |
| 135 | 152 | InterPro | IPR001160 | Peptidase M20C, Xaa-His dipeptidase |
| 159 | 177 | PRINTS | PR00934 | X-His dipeptidase (M25) signature |
| 159 | 177 | InterPro | IPR001160 | Peptidase M20C, Xaa-His dipeptidase |
| 251 | 270 | PRINTS | PR00934 | X-His dipeptidase (M25) signature |
| 251 | 270 | InterPro | IPR001160 | Peptidase M20C, Xaa-His dipeptidase |
| 368 | 484 | FunFam | G3DSA:3.40.630.10:FF:000018 | Aminoacyl-histidine dipeptidase PepD |
| 72 | 480 | Pfam | PF01546 | Peptidase family M20/M25/M40 |
| 72 | 480 | InterPro | IPR002933 | Peptidase M20 |
| 1 | 238 | FunFam | G3DSA:3.40.630.10:FF:000015 | Aminoacyl-histidine dipeptidase PepD |
| 10 | 481 | SUPERFAMILY | SSF53187 | Zn-dependent exopeptidases |
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...
Structural evidence
0 + 2Experimental PDB entries and predicted models. Click Switch to display a different structure in the viewer.
| Entry | Method | Resolution | Chain | Coverage | Links | Status |
|---|---|---|---|---|---|---|
|
AlphaFold
AF_A0A0H3GJV8
|
AlphaFold | — | — | full sequence | — | Viewing |
|
ColabFold
KP13_31631
|
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 |
|---|---|---|---|---|---|---|---|
| 23 | 0.006 | ||||||
| 22 | 0.001 | ||||||
| 26 | 0.001 | ||||||
| 5 | 0.0 |
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 | 33.81 | 0.923 | ||||||
| 2 | 4.76 | 0.173 | ||||||
| 3 | 4.04 | 0.132 | ||||||
| 4 | 1.11 | 0.007 |
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 |
|---|---|---|---|---|---|---|---|
| 14 | 0.594 |
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 | 26.12 | 0.911 | ||||||
| 2 | 2.09 | 0.047 |
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.
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.
No PDB ligands found through similar proteins.
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 |
|---|---|---|---|---|---|
| ZINC1532902 | 0.700 | 206.2 Da LogP -0.86 TPSA 132.1 | ✓ Ro5 | ✓ Clean |
O=C(O)CC[C@@](O)(CC(=O)O)C(=O)O
|
| ZINC2018106 | 0.700 | 206.2 Da LogP -0.86 TPSA 132.1 | ✓ Ro5 | ✓ Clean |
O=C(O)CC[C@](O)(CC(=O)O)C(=O)O
|
| ZINC3593496 | 0.652 | 206.2 Da LogP -1.16 TPSA 121.1 | ✓ Ro5 | ✓ Clean |
COC(=O)C[C@@](O)(CC(=O)O)C(=O)O
|
| ZINC3593497 | 0.652 | 206.2 Da LogP -1.16 TPSA 121.1 | ✓ Ro5 | ✓ Clean |
COC(=O)C[C@](O)(CC(=O)O)C(=O)O
|
| ZINC14686440 | 0.625 | 436.4 Da LogP -2.64 TPSA 247.9 | 1 viol. | ✓ Clean |
O=C(O)C[C@](O)(CC(=O)NCCCCNC(=O)C[C@@](O)(CC(=O…
|
| ZINC14686442 | 0.625 | 436.4 Da LogP -2.64 TPSA 247.9 | 1 viol. | ✓ Clean |
O=C(O)C[C@@](O)(CC(=O)NCCCCNC(=O)C[C@](O)(CC(=O…
|
| ZINC14686444 | 0.625 | 436.4 Da LogP -2.64 TPSA 247.9 | 1 viol. | ✓ Clean |
O=C(O)C[C@@](O)(CC(=O)NCCCCNC(=O)C[C@@](O)(CC(=…
|
| ZINC13398039 | 0.577 | 234.2 Da LogP -0.38 TPSA 121.1 | ✓ Ro5 | ✓ Clean |
CC(C)OC(=O)C[C@](O)(CC(=O)O)C(=O)O
|
| ZINC2528012 | 0.577 | 234.2 Da LogP -0.38 TPSA 121.1 | ✓ Ro5 | ✓ Clean |
CC(C)OC(=O)C[C@@](O)(CC(=O)O)C(=O)O
|
| ZINC146315135 | 0.560 | 204.2 Da LogP 0.86 TPSA 94.8 | ✓ Ro5 | ✓ Clean |
CCCCC[C@@](O)(CC(=O)O)C(=O)O
|
| ZINC146315336 | 0.560 | 204.2 Da LogP 0.86 TPSA 94.8 | ✓ Ro5 | ✓ Clean |
CCCCC[C@](O)(CC(=O)O)C(=O)O
|
| ZINC1850353 | 0.556 | 206.1 Da LogP -0.86 TPSA 132.1 | ✓ Ro5 | ✓ Clean |
O=C(O)CC(O)(CC(=O)O)CC(=O)O
|
| ZINC13398014 | 0.522 | 220.2 Da LogP -1.07 TPSA 110.1 | ✓ Ro5 | ✓ Clean |
COC(=O)CC(O)(CC(=O)OC)C(=O)O
|
| ZINC3861629 | 0.522 | 206.1 Da LogP -1.16 TPSA 121.1 | ✓ Ro5 | ✓ Clean |
COC(=O)C(O)(CC(=O)O)CC(=O)O
|
| ZINC100969993 | 0.500 | 359.5 Da LogP 2.70 TPSA 123.9 | ✓ Ro5 | ✓ Clean |
CCCCCCCCCCCCNC(=O)C[C@](O)(CC(=O)O)C(=O)O
|
| ZINC100969996 | 0.500 | 359.5 Da LogP 2.70 TPSA 123.9 | ✓ Ro5 | ✓ Clean |
CCCCCCCCCCCCNC(=O)C[C@@](O)(CC(=O)O)C(=O)O
|
| ZINC1711854 | 0.500 | 248.2 Da LogP -0.13 TPSA 149.2 | ✓ Ro5 | ✓ Clean |
O=C(O)CC(CC(=O)O)(CC(=O)O)CC(=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.