Overview
Basic information about this protein and its source genome.
- Accession
- PA5260
- Gene
- PA5260 hemC
- Status
- annotated
- Amino acids
- 313
- Structure source
- AlphaFold
Target profile
Computed evidence for target prioritization.
- Human off-target
- hit
- Human identity (%)
- 50.543
- Human E-value
- 2.5499999999999998e-53
- Gut microbiome off-target
- hit
- Essential (DEG)
- Y
- Localization
- Cytoplasmic
Selected Druggability evidence
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.
Sequence
Primary amino-acid sequence viewer.
MSSREIRIATRQSALALWQAEYVKARLEQAHPGLTVTLLPMTSRGDKLLDAPLAKIGGKGLFVKELETALLEGAADIAVHSMKDVPMDFPEGLGLYTICEREDPRDAFVSNTYASLEQLPAGSVVGTSSLRRQAQLLARRPDLQIRFLRGNVNTRLAKLDAGEYDAIILAAAGLIRLGFESRIRSSISVDDSLPAGGQGAVGIECRTADSDLHALLEPLHHTDTALRVTAERALNKRLNGGCQVPIACYAIREGDQLWLRGLVGQPDGTQLLRAEGRAPLAEAEALGVRVAEDLLEQGAEAILEAVYGEAGHP
Functional Annotations
Enzyme classification and Gene Ontology terms linked to this protein.
Enzyme Commission (EC)
1Gene Ontology (GO)
6- GO:0005737 The contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
- GO:0004418 Catalysis of the reaction: H2O + 4 porphobilinogen = hydroxymethylbilane + 4 NH4.
- GO:0006783 The chemical reactions and pathways resulting in the formation of heme, any compound of iron complexed in a porphyrin (tetrapyrrole) ring, from less complex precursors.
- GO:0006782 The chemical reactions and pathways resulting in the formation of protoporphyrinogen IX.
- GO:0018160 The covalent binding of a pyrromethane (dipyrrin) cofactor to protein via the sulfur atom of cysteine forming dipyrrolylmethanemethyl-L-cysteine.
- GO:0033014 The chemical reactions and pathways leading to the formation of tetrapyrroles, natural pigments containing four pyrrole rings joined by one-carbon units linking position 2 of one pyrrole ring to position 5 of the next.
Sequence Features
Domain/signature hits from InterPro and related databases.
Show feature table
| Start | End | DB | Term | Name |
|---|---|---|---|---|
| 226 | 295 | Pfam | PF03900 | Porphobilinogen deaminase, C-terminal domain |
| 226 | 295 | InterPro | IPR022418 | Porphobilinogen deaminase, C-terminal |
| 6 | 212 | Pfam | PF01379 | Porphobilinogen deaminase, dipyromethane cofactor binding domain |
| 6 | 212 | InterPro | IPR022417 | Porphobilinogen deaminase, N-terminal |
| 45 | 65 | PRINTS | PR00151 | Porphobilinogen deaminase signature |
| 45 | 65 | InterPro | IPR000860 | Porphobilinogen deaminase |
| 124 | 141 | PRINTS | PR00151 | Porphobilinogen deaminase signature |
| 124 | 141 | InterPro | IPR000860 | Porphobilinogen deaminase |
| 230 | 247 | PRINTS | PR00151 | Porphobilinogen deaminase signature |
| 230 | 247 | InterPro | IPR000860 | Porphobilinogen deaminase |
| 76 | 95 | PRINTS | PR00151 | Porphobilinogen deaminase signature |
| 76 | 95 | InterPro | IPR000860 | Porphobilinogen deaminase |
| 143 | 160 | PRINTS | PR00151 | Porphobilinogen deaminase signature |
| 143 | 160 | InterPro | IPR000860 | Porphobilinogen deaminase |
| 221 | 310 | Gene3D | G3DSA:3.30.160.40 | - |
| 221 | 310 | InterPro | IPR036803 | Porphobilinogen deaminase, C-terminal domain superfamily |
| 5 | 297 | Hamap | MF_00260 | Porphobilinogen deaminase [hemC]. |
| 5 | 297 | InterPro | IPR000860 | Porphobilinogen deaminase |
| 2 | 306 | PANTHER | PTHR11557 | PORPHOBILINOGEN DEAMINASE |
| 2 | 306 | InterPro | IPR000860 | Porphobilinogen deaminase |
| 104 | 202 | FunFam | G3DSA:3.40.190.10:FF:000005 | Porphobilinogen deaminase |
| 6 | 103 | FunFam | G3DSA:3.40.190.10:FF:000004 | Porphobilinogen deaminase |
| 1 | 311 | PIRSF | PIRSF001438 | PBGD |
| 1 | 311 | InterPro | IPR000860 | Porphobilinogen deaminase |
| 231 | 247 | ProSitePatterns | PS00533 | Porphobilinogen deaminase cofactor-binding site. |
| 231 | 247 | InterPro | IPR022419 | Porphobilinogen deaminase, dipyrromethane cofactor binding site |
| 6 | 210 | Gene3D | G3DSA:3.40.190.10 | - |
| 221 | 310 | FunFam | G3DSA:3.30.160.40:FF:000002 | Porphobilinogen deaminase |
| 103 | 202 | Gene3D | G3DSA:3.40.190.10 | - |
| 5 | 278 | CDD | cd13646 | PBP2_EcHMBS_like |
| 220 | 309 | SUPERFAMILY | SSF54782 | Porphobilinogen deaminase (hydroxymethylbilane synthase), C-terminal domain |
| 220 | 309 | InterPro | IPR036803 | Porphobilinogen deaminase, C-terminal domain superfamily |
| 6 | 297 | NCBIfam | TIGR00212 | hydroxymethylbilane synthase |
| 6 | 297 | InterPro | IPR000860 | Porphobilinogen deaminase |
| 4 | 219 | SUPERFAMILY | SSF53850 | Periplasmic binding protein-like II |
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 + 1Experimental PDB entries and predicted models. Click Switch to display a different structure in the viewer.
| Entry | Method | Resolution | Chain | Coverage | Links | Status |
|---|---|---|---|---|---|---|
|
AlphaFold
PA5260
|
AlphaFold | — | — | full sequence | — | Viewing |
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 |
|---|---|---|---|---|---|---|---|
| 1 | 0.748 | ||||||
| 2 | 0.208 |
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.
| Ligand | Source crystal | UniProt (homolog) | MW · LogP · TPSA | Lipinski | PAINS | SMILES |
|---|---|---|---|---|---|---|
| 18W | Q43316 | 434.4 Da LogP 1.07 TPSA 194.1 | 1 viol. | ✓ Clean |
Cc1c(c(c([nH]1)/C=C\2/C(=C(C(=O)N2)CCC(=O)O)CC(…
|
|
| 29P | Q8GCA8 | 436.4 Da LogP 0.64 TPSA 194.1 | 1 viol. | ✓ Clean |
Cc1c(c(c([nH]1)C[C@H]2C(=C(C(=O)N2)CCC(=O)O)CC(…
|
|
| 7J8 | P08397 | 838.8 Da LogP 2.66 TPSA 361.6 | 2 viol. | ✓ Clean |
Cc1c(c(c([nH]1)Cc2c(c(c([nH]2)Cc3c(c(c([nH]3)Cc…
|
|
| AWQ | Q8GCA8 | 225.2 Da LogP 1.28 TPSA 90.4 | ✓ Ro5 | ✓ Clean |
Cc1c(c(c([nH]1)C)CC(=O)O)CCC(=O)O
|
|
| DPM | P06983 | 420.4 Da LogP 1.53 TPSA 180.8 | 1 viol. | ✓ Clean |
Cc1c(c(c([nH]1)Cc2c(c(c[nH]2)CCC(=O)O)CC(=O)O)C…
|
|
| FWL | P08397 | 352.1 Da LogP 0.72 TPSA 116.4 | ✓ Ro5 | ✓ Clean |
C(CC(=O)O)c1c(c([nH]c1I)CN)CC(=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 |
|---|---|---|---|---|---|
| ZINC56609 | 0.581 | 226.2 Da LogP 0.12 TPSA 116.4 | ✓ Ro5 | ✓ Clean |
NCc1[nH]cc(CCC(=O)O)c1CC(=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.