Amino acids
636
Annotations
7
Features
60
PDB binders
6
Druggability
0.88
Overview
Basic information about this protein and its source genome.
- Accession
- PA4839
- Gene
- PA4839 speA
- Status
- annotated
- Amino acids
- 636
- Structure source
- AlphaFold
EC
GO
GO:0008792 Catalysis of the reaction: L-arginine + H+ = agmatine + CO2.
GO:0046872 Binding to a metal ion.
GO:0006527 The chemical reactions and pathways resulting in the breakdown of L-arginine.
GO:0033388 The chemical reactions and pathways resulting in the formation of putrescine, 1,4-diaminobutane, from other compounds, including arginine.
GO:0008295 The chemical reactions and pathways resulting in the formation of spermidine, N-(3-aminopropyl)-1,4-diaminobutane.
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
- No hit
- Gut microbiome off-target
- hit
- Essential (DEG)
- Y
- Localization
- Unknown
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
0.88
Sequence
Primary amino-acid sequence viewer.
Functional Annotations
Enzyme classification and Gene Ontology terms linked to this protein.
1 EC
6 GO
Enzyme Commission (EC)
1Gene Ontology (GO)
6- GO:0008792 Catalysis of the reaction: L-arginine + H+ = agmatine + CO2.
- GO:0046872 Binding to a metal ion.
- GO:0006527 The chemical reactions and pathways resulting in the breakdown of L-arginine.
- GO:0033388 The chemical reactions and pathways resulting in the formation of putrescine, 1,4-diaminobutane, from other compounds, including arginine.
- GO:0008295 The chemical reactions and pathways resulting in the formation of spermidine, N-(3-aminopropyl)-1,4-diaminobutane.
- 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.
60 records
Show feature table
| Start | End | DB | Term | Name |
|---|---|---|---|---|
| 76 | 352 | Gene3D | G3DSA:3.20.20.10 | Alanine racemase |
| 76 | 352 | InterPro | IPR029066 | PLP-binding barrel |
| 107 | 125 | ProSitePatterns | PS00878 | Orn/DAP/Arg decarboxylases family 2 pyridoxal-P attachment site. |
| 107 | 125 | InterPro | IPR022653 | Orn/DAP/Arg decarboxylase 2, pyridoxal-phosphate binding site |
| 65 | 567 | CDD | cd06830 | PLPDE_III_ADC |
| 65 | 567 | InterPro | IPR002985 | Arginine decarboxylase |
| 1 | 636 | PIRSF | PIRSF001336 | ARGDC |
| 1 | 636 | InterPro | IPR002985 | Arginine decarboxylase |
| 585 | 636 | Gene3D | G3DSA:1.10.287.3440 | - |
| 369 | 461 | FunFam | G3DSA:1.20.58.930:FF:000005 | Biosynthetic arginine decarboxylase |
| 369 | 461 | Gene3D | G3DSA:1.20.58.930 | - |
| 12 | 636 | Hamap | MF_01417 | Biosynthetic arginine decarboxylase [speA]. |
| 12 | 636 | InterPro | IPR002985 | Arginine decarboxylase |
| 376 | 458 | Pfam | PF17810 | Arginine decarboxylase helical bundle domain |
| 376 | 458 | InterPro | IPR040634 | Arginine decarboxylase, helical bundle domain |
| 100 | 350 | Pfam | PF02784 | Pyridoxal-dependent decarboxylase, pyridoxal binding domain |
| 100 | 350 | InterPro | IPR022644 | Orn/DAP/Arg decarboxylase 2, N-terminal |
| 12 | 636 | PANTHER | PTHR43295 | ARGININE DECARBOXYLASE |
| 586 | 635 | Pfam | PF17944 | Arginine decarboxylase C-terminal helical extension |
| 586 | 635 | InterPro | IPR041128 | Arginine decarboxylase, C-terminal helical |
| 75 | 352 | SUPERFAMILY | SSF51419 | PLP-binding barrel |
| 75 | 352 | InterPro | IPR029066 | PLP-binding barrel |
| 468 | 489 | PRINTS | PR01180 | Arginine decarboxylase signature |
| 468 | 489 | InterPro | IPR002985 | Arginine decarboxylase |
| 546 | 567 | PRINTS | PR01180 | Arginine decarboxylase signature |
| 546 | 567 | InterPro | IPR002985 | Arginine decarboxylase |
| 153 | 168 | PRINTS | PR01180 | Arginine decarboxylase signature |
| 153 | 168 | InterPro | IPR002985 | Arginine decarboxylase |
| 179 | 200 | PRINTS | PR01180 | Arginine decarboxylase signature |
| 179 | 200 | InterPro | IPR002985 | Arginine decarboxylase |
| 493 | 518 | PRINTS | PR01180 | Arginine decarboxylase signature |
| 493 | 518 | InterPro | IPR002985 | Arginine decarboxylase |
| 203 | 225 | PRINTS | PR01180 | Arginine decarboxylase signature |
| 203 | 225 | InterPro | IPR002985 | Arginine decarboxylase |
| 99 | 113 | PRINTS | PR01180 | Arginine decarboxylase signature |
| 99 | 113 | InterPro | IPR002985 | Arginine decarboxylase |
| 75 | 90 | PRINTS | PR01180 | Arginine decarboxylase signature |
| 75 | 90 | InterPro | IPR002985 | Arginine decarboxylase |
| 330 | 347 | PRINTS | PR01180 | Arginine decarboxylase signature |
| 330 | 347 | InterPro | IPR002985 | Arginine decarboxylase |
| 440 | 460 | Coils | Coil | Coil |
| 76 | 352 | FunFam | G3DSA:3.20.20.10:FF:000001 | Biosynthetic arginine decarboxylase |
| 459 | 567 | SUPERFAMILY | SSF50621 | Alanine racemase C-terminal domain-like |
| 459 | 567 | InterPro | IPR009006 | Alanine racemase/group IV decarboxylase, C-terminal |
| 130 | 142 | PRINTS | PR01179 | Ornithine/diaminopimelate/arginine (ODA) decarboxylase family signature |
| 130 | 142 | InterPro | IPR000183 | Ornithine/DAP/Arg decarboxylase |
| 340 | 359 | PRINTS | PR01179 | Ornithine/diaminopimelate/arginine (ODA) decarboxylase family signature |
| 340 | 359 | InterPro | IPR000183 | Ornithine/DAP/Arg decarboxylase |
| 107 | 125 | PRINTS | PR01179 | Ornithine/diaminopimelate/arginine (ODA) decarboxylase family signature |
| 107 | 125 | InterPro | IPR000183 | Ornithine/DAP/Arg decarboxylase |
| 246 | 259 | PRINTS | PR01179 | Ornithine/diaminopimelate/arginine (ODA) decarboxylase family signature |
| 246 | 259 | InterPro | IPR000183 | Ornithine/DAP/Arg decarboxylase |
| 546 | 559 | PRINTS | PR01179 | Ornithine/diaminopimelate/arginine (ODA) decarboxylase family signature |
| 546 | 559 | InterPro | IPR000183 | Ornithine/DAP/Arg decarboxylase |
| 14 | 636 | NCBIfam | TIGR01273 | arginine decarboxylase |
| 14 | 636 | InterPro | IPR002985 | Arginine decarboxylase |
| 23 | 572 | Gene3D | G3DSA:2.40.37.10 | Lyase, Ornithine Decarboxylase; Chain A, domain 1 |
| 23 | 572 | InterPro | IPR009006 | Alanine racemase/group IV decarboxylase, C-terminal |
| 282 | 297 | ProSitePatterns | PS00879 | Orn/DAP/Arg decarboxylases family 2 signature 2. |
| 282 | 297 | InterPro | IPR022657 | Orn/DAP/Arg decarboxylase 2, conserved site |
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
PA4839
|
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 |
|---|---|---|---|---|---|---|---|
| 17 | 0.88 | ||||||
| 15 | 0.797 | ||||||
| 3 | 0.392 |
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.
56 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 |
|---|---|---|---|---|---|---|
| AG2 | Q7MK24 | 130.2 Da LogP -0.79 TPSA 87.9 | ✓ Ro5 | ✓ Clean |
C(CCNC(=N)N)CN
|
|
| AZ1 | Q58497 | 188.2 Da LogP 1.89 TPSA 74.6 | ✓ Ro5 | ✓ Clean |
C(CCCC(=O)O)CCCC(=O)O
|
|
| DN9 | A0A0H3JPF2 | 465.4 Da LogP -1.41 TPSA 235.8 | 1 viol. | ✓ Clean |
Cc1c(c(c(cn1)COP(=O)(O)O)CNCCNC(=O)C[C@](CC(=O)…
|
|
| LLP | A1SR00 | 375.3 Da LogP 0.71 TPSA 175.6 | ✓ Ro5 | ✓ Clean |
Cc1c(c(c(cn1)COP(=O)(O)O)/C=N/CCCCC(C(=O)O)N)O
|
|
| TME | A1SR00 | 44.1 Da LogP 1.42 TPSA 0.0 | ✓ Ro5 | ✓ Clean |
CCC
|
|
| X3J | A0A0H3JPF2 | 234.2 Da LogP -2.26 TPSA 150.0 | ✓ Ro5 | ✓ Clean |
C(CNC(=O)C[C@](CC(=O)O)(C(=O)O)O)N
|
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 |
|---|---|---|---|---|---|
| ZINC1529497 | 1.000 | 230.3 Da LogP 3.06 TPSA 74.6 | ✓ Ro5 | ✓ Clean |
O=C(O)CCCCCCCCCCC(=O)O
|
| ZINC1531045 | 1.000 | 202.2 Da LogP 2.28 TPSA 74.6 | ✓ Ro5 | ✓ Clean |
O=C(O)CCCCCCCCC(=O)O
|
| ZINC1593115 | 1.000 | 216.3 Da LogP 2.67 TPSA 74.6 | ✓ Ro5 | ✓ Clean |
O=C(O)CCCCCCCCCC(=O)O
|
| ZINC1700020 | 1.000 | 244.3 Da LogP 3.45 TPSA 74.6 | ✓ Ro5 | ✓ Clean |
O=C(O)CCCCCCCCCCCC(=O)O
|
| ZINC3860440 | 1.000 | 258.4 Da LogP 3.84 TPSA 74.6 | ✓ Ro5 | ✓ Clean |
O=C(O)CCCCCCCCCCCCC(=O)O
|
| ZINC3861298 | 1.000 | 286.4 Da LogP 4.62 TPSA 74.6 | ✓ Ro5 | ✓ Clean |
O=C(O)CCCCCCCCCCCCCCC(=O)O
|
| ZINC5113062 | 1.000 | 272.4 Da LogP 4.23 TPSA 74.6 | ✓ Ro5 | ✓ Clean |
O=C(O)CCCCCCCCCCCCCC(=O)O
|
| ZINC26897400 | 0.800 | 286.4 Da LogP 3.41 TPSA 91.7 | ✓ Ro5 | ✓ Clean |
O=C(O)CCCCCCC(=O)CCCCCCC(=O)O
|
| ZINC3074813 | 0.800 | 258.3 Da LogP 2.63 TPSA 91.7 | ✓ Ro5 | ✓ Clean |
O=C(O)CCCCCC(=O)CCCCCC(=O)O
|
| ZINC34423725 | 0.800 | 342.5 Da LogP 4.97 TPSA 91.7 | ✓ Ro5 | ✓ Clean |
O=C(O)CCCCCCCCC(=O)CCCCCCCCC(=O)O
|
| ZINC4822898 | 0.800 | 272.3 Da LogP 3.02 TPSA 91.7 | ✓ Ro5 | ✓ Clean |
O=C(O)CCCCCCC(=O)CCCCCC(=O)O
|
| ZINC4822900 | 0.800 | 300.4 Da LogP 3.80 TPSA 91.7 | ✓ Ro5 | ✓ Clean |
O=C(O)CCCCCCCCC(=O)CCCCCC(=O)O
|
| ZINC14686440 | 0.759 | 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 | 0.759 | 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 | 0.759 | 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(=…
|
| ZINC13433578 | 0.750 | 201.3 Da LogP 1.68 TPSA 80.4 | ✓ Ro5 | ✓ Clean |
NC(=O)CCCCCCCCC(=O)O
|
| ZINC14510370 | 0.750 | 244.4 Da LogP 3.74 TPSA 57.5 | ✓ Ro5 | ✓ Clean |
O=C(O)CCCCCCCCCCCCCO
|
| ZINC1531061 | 0.750 | 216.3 Da LogP 2.96 TPSA 57.5 | ✓ Ro5 | ✓ Clean |
O=C(O)CCCCCCCCCCCO
|
| ZINC1610426 | 0.750 | 230.3 Da LogP 3.35 TPSA 57.5 | ✓ Ro5 | ✓ Clean |
O=C(O)CCCCCCCCCCCCO
|
| ZINC2168567 | 0.750 | 202.3 Da LogP 2.57 TPSA 57.5 | ✓ Ro5 | ✓ Clean |
O=C(O)CCCCCCCCCCO
|
| ZINC3074815 | 0.750 | 230.3 Da LogP 1.85 TPSA 91.7 | ✓ Ro5 | ✓ Clean |
O=C(O)CCCCCC(=O)CCCC(=O)O
|
| ZINC3861297 | 0.750 | 272.4 Da LogP 4.52 TPSA 57.5 | ✓ Ro5 | ✓ Clean |
O=C(O)CCCCCCCCCCCCCCCO
|
| ZINC4284502 | 0.750 | 258.4 Da LogP 4.13 TPSA 57.5 | ✓ Ro5 | ✓ Clean |
O=C(O)CCCCCCCCCCCCCCO
|
| ZINC5287109 | 0.750 | 286.5 Da LogP 4.91 TPSA 57.5 | ✓ Ro5 | ✓ Clean |
O=C(O)CCCCCCCCCCCCCCCCO
|
| ZINC13545924 | 0.737 | 214.3 Da LogP -0.10 TPSA 123.8 | 1 viol. | ✓ Clean |
N=C(N)NCCCCCCCNC(=N)N
|
| ZINC1561855 | 0.737 | 200.3 Da LogP -0.49 TPSA 123.8 | 1 viol. | ✓ Clean |
N=C(N)NCCCCCCNC(=N)N
|
| ZINC2013578 | 0.737 | 228.3 Da LogP 0.29 TPSA 123.8 | 1 viol. | ✓ Clean |
N=C(N)NCCCCCCCCNC(=N)N
|
| ZINC3995661 | 0.737 | 256.4 Da LogP 1.07 TPSA 123.8 | 1 viol. | ✓ Clean |
N=C(N)NCCCCCCCCCCNC(=N)N
|
| ZINC2508031 | 0.733 | 230.3 Da LogP 1.85 TPSA 91.7 | ✓ Ro5 | ✓ Clean |
O=C(O)CCCCC(=O)CCCCC(=O)O
|
| ZINC2114966 | 0.724 | 332.2 Da LogP 0.99 TPSA 149.5 | ✓ Ro5 | ✓ Clean |
Cc1ncc(COP(=O)(O)O)c(/C=N/CCCC(=O)O)c1O
|
| ZINC12954423 | 0.706 | 232.4 Da LogP 3.90 TPSA 37.3 | ✓ Ro5 | ✓ Clean |
O=C(O)CCCCCCCCCCCS
|
| ZINC13357569 | 0.706 | 243.4 Da LogP 3.71 TPSA 63.3 | ✓ Ro5 | ✓ Clean |
NCCCCCCCCCCCCCC(=O)O
|
| ZINC138216182 | 0.706 | 293.2 Da LogP 4.76 TPSA 37.3 | ✓ Ro5 | ✓ Clean |
O=C(O)CCCCCCCCCCCCBr
|
| ZINC14619253 | 0.706 | 214.3 Da LogP 3.17 TPSA 54.4 | ✓ Ro5 | ✓ Clean |
CC(=O)CCCCCCCCCC(=O)O
|
| ZINC1529498 | 0.706 | 200.3 Da LogP 3.99 TPSA 37.3 | ✓ Ro5 | ✓ Clean |
CCCCCCCCCCCC(=O)O
|
| ZINC1530417 | 0.706 | 228.4 Da LogP 4.77 TPSA 37.3 | ✓ Ro5 | ✓ Clean |
CCCCCCCCCCCCCC(=O)O
|
| ZINC1628119 | 0.706 | 214.3 Da LogP 4.38 TPSA 37.3 | ✓ Ro5 | ✓ Clean |
CCCCCCCCCCCCC(=O)O
|
| ZINC1763117 | 0.706 | 201.3 Da LogP 2.54 TPSA 63.3 | ✓ Ro5 | ✓ Clean |
NCCCCCCCCCCC(=O)O
|
| ZINC1841307 | 0.706 | 228.3 Da LogP 3.56 TPSA 54.4 | ✓ Ro5 | ✓ Clean |
CC(=O)CCCCCCCCCCC(=O)O
|
| ZINC1845814 | 0.706 | 215.3 Da LogP 2.93 TPSA 63.3 | ✓ Ro5 | ✓ Clean |
NCCCCCCCCCCCC(=O)O
|
| ZINC1845839 | 0.706 | 200.3 Da LogP 2.78 TPSA 54.4 | ✓ Ro5 | ✓ Clean |
CC(=O)CCCCCCCCC(=O)O
|
| ZINC2164257 | 0.706 | 218.4 Da LogP 3.51 TPSA 37.3 | ✓ Ro5 | ✓ Clean |
O=C(O)CCCCCCCCCCS
|
| ZINC22048354 | 0.706 | 229.4 Da LogP 3.32 TPSA 63.3 | ✓ Ro5 | ✓ Clean |
NCCCCCCCCCCCCC(=O)O
|
| ZINC33822328 | 0.706 | 270.4 Da LogP 4.73 TPSA 54.4 | ✓ Ro5 | ✓ Clean |
CC(=O)CCCCCCCCCCCCCC(=O)O
|
| ZINC34552398 | 0.706 | 257.4 Da LogP 4.10 TPSA 63.3 | ✓ Ro5 | ✓ Clean |
NCCCCCCCCCCCCCCC(=O)O
|
| ZINC34628306 | 0.706 | 271.4 Da LogP 4.49 TPSA 63.3 | ✓ Ro5 | ✓ Clean |
NCCCCCCCCCCCCCCCC(=O)O
|
| ZINC35465466 | 0.706 | 244.3 Da LogP 2.24 TPSA 91.7 | ✓ Ro5 | ✓ Clean |
O=C(O)CCCCCCCC(=O)CCC(=O)O
|
| ZINC5855130 | 0.706 | 242.4 Da LogP 3.95 TPSA 54.4 | ✓ Ro5 | ✓ Clean |
CC(=O)CCCCCCCCCCCC(=O)O
|
| ZINC90745150 | 0.706 | 260.4 Da LogP 4.68 TPSA 37.3 | ✓ Ro5 | ✓ Clean |
O=C(O)CCCCCCCCCCCCCS
|
| ZINC5501162 | 0.667 | 350.5 Da LogP 4.52 TPSA 74.6 | ✓ Ro5 | ✓ Clean |
O=C(O)CCCCSCCCCCCSCCCCC(=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.