Protein profile
PA0530
class III pyridoxal phosphate-dependent aminotransferase
Genome: NC_002516.2
Amino acids
393
Annotations
4
Features
19
PDB binders
15
Druggability
0.333
Overview
Basic information about this protein and its source genome.
- Accession
- PA0530
- Gene
- PA0530
- Status
- annotated
- Amino acids
- 393
- Structure source
- AlphaFold
GO
GO:0042802 Binding to an identical protein or proteins.
GO:0030170 Binding to pyridoxal 5' phosphate, 3-hydroxy-5-(hydroxymethyl)-2-methyl4-pyridine carboxaldehyde 5' phosphate, the biologically active form of vitamin B6.
GO:0008483 Catalysis of the transfer of an amino group to an acceptor, usually a 2-oxo acid.
GO:0003824 Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
Target profile
Computed evidence for target prioritization.
- Human off-target
- hit
- Human identity (%)
- 30.214
- Human E-value
- 3.67e-46
- Gut microbiome off-target
- hit
- Essential (DEG)
- N
- Localization
- CytoplasmicMembrane
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.
FPocket
0.333
Sequence
Primary amino-acid sequence viewer.
Functional Annotations
Enzyme classification and Gene Ontology terms linked to this protein.
4 GO
Gene Ontology (GO)
4- GO:0042802 Binding to an identical protein or proteins.
- GO:0030170 Binding to pyridoxal 5' phosphate, 3-hydroxy-5-(hydroxymethyl)-2-methyl4-pyridine carboxaldehyde 5' phosphate, the biologically active form of vitamin B6.
- GO:0008483 Catalysis of the transfer of an amino group to an acceptor, usually a 2-oxo acid.
- GO:0003824 Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
Sequence Features
Domain/signature hits from InterPro and related databases.
19 records
Show feature table
| Start | End | DB | Term | Name |
|---|---|---|---|---|
| 368 | 393 | Coils | Coil | Coil |
| 20 | 382 | CDD | cd00610 | OAT_like |
| 20 | 382 | InterPro | IPR005814 | Aminotransferase class-III |
| 23 | 375 | Gene3D | G3DSA:3.90.1150.10 | Aspartate Aminotransferase, domain 1 |
| 23 | 375 | InterPro | IPR015422 | Pyridoxal phosphate-dependent transferase, small domain |
| 19 | 382 | Pfam | PF00202 | Aminotransferase class-III |
| 19 | 382 | InterPro | IPR005814 | Aminotransferase class-III |
| 53 | 291 | FunFam | G3DSA:3.40.640.10:FF:000160 | Class III pyridoxal phosphate-dependent aminotransferase |
| 157 | 385 | PIRSF | PIRSF000521 | Transaminase_4ab_Lys_Orn |
| 157 | 385 | InterPro | IPR005814 | Aminotransferase class-III |
| 2 | 142 | PIRSF | PIRSF000521 | Transaminase_4ab_Lys_Orn |
| 2 | 142 | InterPro | IPR005814 | Aminotransferase class-III |
| 53 | 291 | Gene3D | G3DSA:3.40.640.10 | - |
| 53 | 291 | InterPro | IPR015421 | Pyridoxal phosphate-dependent transferase, major domain |
| 14 | 384 | SUPERFAMILY | SSF53383 | PLP-dependent transferases |
| 14 | 384 | InterPro | IPR015424 | Pyridoxal phosphate-dependent transferase |
| 11 | 387 | PANTHER | PTHR11986 | AMINOTRANSFERASE CLASS III |
| 210 | 247 | ProSitePatterns | PS00600 | Aminotransferases class-III pyridoxal-phosphate attachment site. |
| 210 | 247 | InterPro | IPR005814 | Aminotransferase class-III |
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 + 1Experimental PDB entries and predicted models. Click Switch to display a different structure in the viewer.
| Entry | Method | Resolution | Chain | Coverage | Links | Status |
|---|---|---|---|---|---|---|
|
AlphaFold
PA0530
|
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 |
|---|---|---|---|---|---|---|---|
| 2 | 0.333 |
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.
65 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 |
|---|---|---|---|---|---|---|
| 5PA | P16932 | 332.2 Da LogP 0.41 TPSA 149.2 | ✓ Ro5 | ✓ Clean |
Cc1c(c(c(cn1)COP(=O)(O)O)CNC2(CC2)C(=O)O)O
|
|
| DCS | P16932 | 333.2 Da LogP -0.78 TPSA 150.2 | ✓ Ro5 | ✓ Clean |
Cc1c(c(c(cn1)COP(=O)(O)O)CN[C@@H]2CONC2=O)O
|
|
| ELP | P16932 | 430.3 Da LogP 2.17 TPSA 169.8 | ✓ Ro5 | ✓ Clean |
Cc1c(c(c(cn1)COP(=O)(O)O)C=N[C@@](C)(c2ccccc2)P…
|
|
| EPC | P16932 | 354.2 Da LogP 0.65 TPSA 169.8 | ✓ Ro5 | ✓ Clean |
Cc1c(c(c(cn1)COP(=O)(O)O)\C=N\[C@H](C)P(=O)(O)O…
|
|
| HCP | P16932 | 394.3 Da LogP 1.57 TPSA 169.8 | ✓ Ro5 | ✓ Clean |
Cc1c(c(c(cn1)COP(=O)(O)O)C=NC2(CCCC2)P(=O)(O)O)O
|
|
| LCS | P16932 | 331.2 Da LogP -0.29 TPSA 150.6 | ✓ Ro5 | ✓ Clean |
Cc1c(c(c(cn1)COP(=O)(O)O)C/N=C/2\CONC2=O)O
|
|
| MPM | P16932 | 382.2 Da LogP 1.43 TPSA 169.8 | ✓ Ro5 | ✓ Clean |
CC[C@](C)(/N=C/c1c(cnc(c1O)C)COP(=O)(O)O)P(=O)(…
|
|
| NMA | P16932 | 334.3 Da LogP 0.66 TPSA 149.2 | ✓ Ro5 | ✓ Clean |
Cc1c(c(c(cn1)COP(=O)(O)O)CNC(C)(C)C(=O)O)O
|
|
| P00 | P40732 | 363.3 Da LogP -0.14 TPSA 184.8 | ✓ Ro5 | ✓ Clean |
Cc1c(c(c(cn1)COP(=O)(O)O)/C=N/OCC[C@@H](C(=O)O)…
|
|
| PMP | P16932 | 248.2 Da LogP 0.16 TPSA 125.9 | ✓ Ro5 | ✓ Clean |
Cc1c(c(c(cn1)COP(=O)(O)O)CN)O
|
|
| POI | Q5SHH5 | 405.3 Da LogP 0.16 TPSA 178.3 | 1 viol. | ✓ Clean |
Cc1c(c(c(cn1)COP(=O)(O)O)CNCCC[C@@H](C(=O)O)NC(…
|
|
| PPE | Q5SHH5 | 379.3 Da LogP -0.47 TPSA 187.8 | 1 viol. | ✓ Clean |
Cc1c(c(c(c[nH+]1)COP(=O)(O)O)CN[C@@H](CCC(=O)O)…
|
|
| PXG | P40732 | 368.3 Da LogP 2.02 TPSA 149.2 | ✓ Ro5 | ✓ Clean |
Cc1c(c(c(cn1)COP(=O)(O)O)CNc2cccc(c2)C(=O)O)O
|
|
| SUO | P77581 | 232.2 Da LogP -0.84 TPSA 129.7 | ✓ Ro5 | ✓ Clean |
C(C[C@@H](C(=O)O)NC(=O)CCC(=O)O)CN
|
|
| TNF | P40732 | 229.1 Da LogP 1.12 TPSA 149.7 | ✓ Ro5 | ✓ Clean |
c1c(cc(c(c1[N+](=O)[O-])O)[N+](=O)[O-])[N+](=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 |
|---|---|---|---|---|---|
| ZINC1883067 | 1.000 | 229.1 Da LogP 1.12 TPSA 149.7 | ✓ Ro5 | ✓ Clean |
O=[N+]([O-])c1cc([N+](=O)[O-])c(O)c([N+](=O)[O-…
|
| ZINC2170217 | 0.792 | 200.1 Da LogP 0.91 TPSA 126.7 | ✓ Ro5 | Alert |
O=[N+]([O-])c1cc(O)c(O)c([N+](=O)[O-])c1
|
| ZINC68564159 | 0.792 | 366.2 Da LogP 2.40 TPSA 213.0 | ✓ Ro5 | ✓ Clean |
O=[N+]([O-])c1cc(-c2cc([N+](=O)[O-])cc([N+](=O)…
|
| ZINC34772749 | 0.769 | 228.1 Da LogP 0.91 TPSA 143.8 | ✓ Ro5 | ✓ Clean |
O=C(O)c1cc([N+](=O)[O-])cc([N+](=O)[O-])c1O
|
| ZINC1866114950 | 0.758 | 260.3 Da LogP -0.06 TPSA 129.7 | ✓ Ro5 | ✓ Clean |
NCCCC[C@H](NC(=O)CCCC(=O)O)C(=O)O
|
| ZINC1555225 | 0.731 | 218.6 Da LogP 1.86 TPSA 106.5 | ✓ Ro5 | ✓ Clean |
O=[N+]([O-])c1cc(Cl)c(O)c([N+](=O)[O-])c1
|
| ZINC1657271 | 0.731 | 263.0 Da LogP 1.97 TPSA 106.5 | ✓ Ro5 | ✓ Clean |
O=[N+]([O-])c1cc(Br)c(O)c([N+](=O)[O-])c1
|
| ZINC34261082 | 0.731 | 202.1 Da LogP 1.35 TPSA 106.5 | ✓ Ro5 | ✓ Clean |
O=[N+]([O-])c1cc(F)c(O)c([N+](=O)[O-])c1
|
| ZINC1530138 | 0.719 | 217.3 Da LogP -0.97 TPSA 118.4 | ✓ Ro5 | ✓ Clean |
NCCCC[C@H](NC(=O)CCN)C(=O)O
|
| ZINC15261541 | 0.706 | 261.3 Da LogP -1.51 TPSA 155.7 | ✓ Ro5 | ✓ Clean |
NCCC[C@H](NC(=O)CC[C@H](N)C(=O)O)C(=O)O
|
| ZINC104057557 | 0.704 | 378.2 Da LogP 2.26 TPSA 209.9 | ✓ Ro5 | ✓ Clean |
O=C(c1cc([N+](=O)[O-])cc([N+](=O)[O-])c1)c1cc([…
|
| ZINC1530296 | 0.700 | 247.2 Da LogP -0.71 TPSA 141.0 | ✓ Ro5 | ✓ Clean |
O=C(O)CCC(=O)N[C@@H](CCC(=O)O)C(=O)O
|
| 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
|
| ZINC6783254 | 0.697 | 231.2 Da LogP 0.61 TPSA 103.7 | ✓ Ro5 | ✓ Clean |
CCCC[C@H](NC(=O)CCC(=O)O)C(=O)O
|
| ZINC6783285 | 0.697 | 231.2 Da LogP 0.61 TPSA 103.7 | ✓ Ro5 | ✓ Clean |
CCCC[C@@H](NC(=O)CCC(=O)O)C(=O)O
|
| ZINC3080634 | 0.696 | 200.1 Da LogP 0.91 TPSA 126.7 | ✓ Ro5 | ✓ Clean |
O=[N+]([O-])c1cc(O)cc([N+](=O)[O-])c1O
|
| ZINC43450378 | 0.696 | 366.2 Da LogP 2.40 TPSA 213.0 | ✓ Ro5 | ✓ Clean |
O=[N+]([O-])c1cc(-c2cc([N+](=O)[O-])c(O)c([N+](…
|
| ZINC1841206 | 0.679 | 212.1 Da LogP 1.02 TPSA 123.6 | ✓ Ro5 | ✓ Clean |
O=Cc1cc([N+](=O)[O-])cc([N+](=O)[O-])c1O
|
| ZINC32250330 | 0.679 | 214.1 Da LogP 0.70 TPSA 126.7 | ✓ Ro5 | ✓ Clean |
O=[N+]([O-])c1cc(CO)c(O)c([N+](=O)[O-])c1
|
| ZINC5956205 | 0.679 | 212.2 Da LogP 1.77 TPSA 106.5 | ✓ Ro5 | ✓ Clean |
CCc1cc([N+](=O)[O-])cc([N+](=O)[O-])c1O
|
| ZINC100924232 | 0.667 | 292.0 Da LogP 2.17 TPSA 129.4 | ✓ Ro5 | ✓ Clean |
O=[N+]([O-])c1cc([N+](=O)[O-])c(Br)c([N+](=O)[O…
|
| ZINC141957116 | 0.667 | 342.5 Da LogP 4.00 TPSA 92.4 | ✓ Ro5 | ✓ Clean |
CCCCCCCCCCCCCC(=O)N[C@@H](CCCN)C(=O)O
|
| ZINC1737586 | 0.667 | 242.1 Da LogP 1.00 TPSA 132.8 | ✓ Ro5 | ✓ Clean |
COC(=O)c1cc([N+](=O)[O-])cc([N+](=O)[O-])c1O
|
| ZINC3161143 | 0.667 | 255.2 Da LogP 0.91 TPSA 126.8 | ✓ Ro5 | ✓ Clean |
CN(C)C(=O)c1cc([N+](=O)[O-])cc([N+](=O)[O-])c1O
|
| ZINC3161144 | 0.667 | 241.2 Da LogP 0.57 TPSA 135.6 | ✓ Ro5 | ✓ Clean |
CNC(=O)c1cc([N+](=O)[O-])cc([N+](=O)[O-])c1O
|
| ZINC78044048 | 0.667 | 342.5 Da LogP 4.00 TPSA 92.4 | ✓ Ro5 | ✓ Clean |
CCCCCCCCCCCCCC(=O)N[C@H](CCCN)C(=O)O
|
| ZINC1655733 | 0.655 | 240.2 Da LogP 2.51 TPSA 106.5 | ✓ Ro5 | ✓ Clean |
CC(C)(C)c1cc([N+](=O)[O-])cc([N+](=O)[O-])c1O
|
| ZINC1687159 | 0.655 | 226.2 Da LogP 2.33 TPSA 106.5 | ✓ Ro5 | ✓ Clean |
CC(C)c1cc([N+](=O)[O-])cc([N+](=O)[O-])c1O
|
| ZINC4343573 | 0.655 | 214.1 Da LogP 1.22 TPSA 115.7 | ✓ Ro5 | ✓ Clean |
COc1cc([N+](=O)[O-])cc([N+](=O)[O-])c1O
|
| ZINC59195086 | 0.655 | 242.1 Da LogP 0.84 TPSA 143.8 | ✓ Ro5 | ✓ Clean |
O=C(O)Cc1cc([N+](=O)[O-])cc([N+](=O)[O-])c1O
|
| ZINC104179173 | 0.652 | 424.2 Da LogP 2.80 TPSA 258.8 | 1 viol. | ✓ Clean |
O=[N+]([O-])c1cc([N+](=O)[O-])c(-c2c([N+](=O)[O…
|
| ZINC2149898 | 0.652 | 216.1 Da LogP 0.62 TPSA 147.0 | ✓ Ro5 | Alert |
O=[N+]([O-])c1cc([N+](=O)[O-])c(O)c(O)c1O
|
| 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
|
| ZINC1529628 | 0.649 | 274.3 Da LogP -1.32 TPSA 165.6 | 1 viol. | ✓ Clean |
N=C(N)NCCC[C@H](NC(=O)CCC(=O)O)C(=O)O
|
| ZINC3156562 | 0.645 | 283.2 Da LogP 1.74 TPSA 135.6 | ✓ Ro5 | ✓ Clean |
CC(C)(C)NC(=O)c1cc([N+](=O)[O-])cc([N+](=O)[O-]…
|
| ZINC66139505 | 0.643 | 305.2 Da LogP 2.78 TPSA 149.7 | ✓ Ro5 | ✓ Clean |
O=[N+]([O-])c1ccc(-c2cc([N+](=O)[O-])c(O)c([N+]…
|
| ZINC104122301 | 0.640 | 454.2 Da LogP 2.57 TPSA 282.9 | 1 viol. | ✓ Clean |
O=[N+]([O-])c1cc([N+](=O)[O-])c(NNc2c([N+](=O)[…
|
| ZINC1693336 | 0.640 | 218.6 Da LogP 1.86 TPSA 106.5 | ✓ Ro5 | ✓ Clean |
O=[N+]([O-])c1cc(Cl)cc([N+](=O)[O-])c1O
|
| ZINC1706150 | 0.640 | 202.1 Da LogP 1.35 TPSA 106.5 | ✓ Ro5 | ✓ Clean |
O=[N+]([O-])c1cc(F)cc([N+](=O)[O-])c1O
|
| ZINC34328127 | 0.640 | 263.0 Da LogP 1.97 TPSA 106.5 | ✓ Ro5 | ✓ Clean |
O=[N+]([O-])c1cc(Br)cc([N+](=O)[O-])c1O
|
| ZINC5113904 | 0.639 | 261.3 Da LogP -1.51 TPSA 155.7 | ✓ Ro5 | ✓ Clean |
NCCC[C@H](NC(=O)[C@@H](N)CCC(=O)O)C(=O)O
|
| ZINC147300883 | 0.636 | 217.2 Da LogP 0.22 TPSA 103.7 | ✓ Ro5 | ✓ Clean |
CCC[C@@H](NC(=O)CCC(=O)O)C(=O)O
|
| ZINC24803120 | 0.636 | 217.2 Da LogP 0.22 TPSA 103.7 | ✓ Ro5 | ✓ Clean |
CCC[C@H](NC(=O)CCC(=O)O)C(=O)O
|
| ZINC100006785 | 0.630 | 256.1 Da LogP 0.51 TPSA 172.5 | ✓ Ro5 | ✓ Clean |
NC(=O)c1c([N+](=O)[O-])cc([N+](=O)[O-])cc1[N+](…
|
| ZINC116981435 | 0.629 | 319.3 Da LogP -0.81 TPSA 179.0 | 1 viol. | ✓ Clean |
NCCCC[C@@H](NC(=O)N[C@@H](CCC(=O)O)C(=O)O)C(=O)O
|
| ZINC116981437 | 0.629 | 319.3 Da LogP -0.81 TPSA 179.0 | 1 viol. | ✓ Clean |
NCCCC[C@@H](NC(=O)N[C@H](CCC(=O)O)C(=O)O)C(=O)O
|
| ZINC116981440 | 0.629 | 319.3 Da LogP -0.81 TPSA 179.0 | 1 viol. | ✓ Clean |
NCCCC[C@H](NC(=O)N[C@H](CCC(=O)O)C(=O)O)C(=O)O
|
| ZINC40860752 | 0.629 | 319.3 Da LogP -0.81 TPSA 179.0 | 1 viol. | ✓ Clean |
NCCCC[C@H](NC(=O)N[C@@H](CCC(=O)O)C(=O)O)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.