Protein profile
PA5565
tRNA uridine 5-carboxymethylaminomethyl modification protein GidA
Genome: NC_002516.2
Amino acids
630
Annotations
5
Features
31
PDB binders
2
Druggability
0.442
Overview
Basic information about this protein and its source genome.
- Accession
- PA5565
- Gene
- mnmG gidA PA5565
- Status
- annotated
- Amino acids
- 630
- Structure source
- AlphaFold
GO
GO:0005829 The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
GO:0050660 Binding to FAD, flavin-adenine dinucleotide, the coenzyme or the prosthetic group of various flavoprotein oxidoreductase enzymes, in either the oxidized form, FAD, or the reduced form, FADH2.
GO:0030488 The posttranscriptional addition of methyl groups to specific residues in a tRNA molecule.
GO:0002098 The process in which a uridine at position 34 of a tRNA is post-transcriptionally modified. The wobble nucleoside of the tRNA sequence (position 34) corresponds to the first position of the anticodon.
GO:0008033 The process in which a pre-tRNA molecule is converted to a mature tRNA, ready for addition of an aminoacyl group.
Target profile
Computed evidence for target prioritization.
- Human off-target
- hit
- Human identity (%)
- 78.947
- Human E-value
- 6.71e-06
- 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.
FPocket
0.442
Sequence
Primary amino-acid sequence viewer.
Functional Annotations
Enzyme classification and Gene Ontology terms linked to this protein.
5 GO
Gene Ontology (GO)
5- GO:0005829 The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
- GO:0050660 Binding to FAD, flavin-adenine dinucleotide, the coenzyme or the prosthetic group of various flavoprotein oxidoreductase enzymes, in either the oxidized form, FAD, or the reduced form, FADH2.
- GO:0030488 The posttranscriptional addition of methyl groups to specific residues in a tRNA molecule.
- GO:0002098 The process in which a uridine at position 34 of a tRNA is post-transcriptionally modified. The wobble nucleoside of the tRNA sequence (position 34) corresponds to the first position of the anticodon.
- GO:0008033 The process in which a pre-tRNA molecule is converted to a mature tRNA, ready for addition of an aminoacyl group.
Sequence Features
Domain/signature hits from InterPro and related databases.
31 records
Show feature table
| Start | End | DB | Term | Name |
|---|---|---|---|---|
| 7 | 620 | NCBIfam | TIGR00136 | tRNA uridine-5-carboxymethylaminomethyl(34) synthesis enzyme MnmG |
| 7 | 620 | InterPro | IPR004416 | tRNA uridine 5-carboxymethylaminomethyl modification enzyme MnmG |
| 273 | 287 | ProSitePatterns | PS01280 | Glucose inhibited division protein A family signature 1. |
| 273 | 287 | InterPro | IPR020595 | MnmG-related, conserved site |
| 294 | 458 | Gene3D | G3DSA:3.50.50.60 | - |
| 294 | 458 | InterPro | IPR036188 | FAD/NAD(P)-binding domain superfamily |
| 2 | 232 | Gene3D | G3DSA:3.50.50.60 | - |
| 2 | 232 | InterPro | IPR036188 | FAD/NAD(P)-binding domain superfamily |
| 459 | 557 | Gene3D | G3DSA:1.10.10.1800 | - |
| 295 | 458 | FunFam | G3DSA:3.50.50.60:FF:000002 | tRNA uridine 5-carboxymethylaminomethyl modification enzyme MnmG |
| 368 | 391 | ProSitePatterns | PS01281 | Glucose inhibited division protein A family signature 2. |
| 368 | 391 | InterPro | IPR020595 | MnmG-related, conserved site |
| 567 | 619 | Gene3D | G3DSA:1.10.150.570 | - |
| 567 | 619 | InterPro | IPR044920 | tRNA uridine 5-carboxymethylaminomethyl modification enzyme, C-terminal subdomain superfamily |
| 6 | 625 | PANTHER | PTHR11806 | GLUCOSE INHIBITED DIVISION PROTEIN A |
| 6 | 625 | InterPro | IPR002218 | tRNA uridine 5-carboxymethylaminomethyl modification enzyme MnmG-related |
| 2 | 233 | FunFam | G3DSA:3.50.50.60:FF:000010 | tRNA uridine 5-carboxymethylaminomethyl modification enzyme MnmG |
| 8 | 399 | Pfam | PF01134 | Glucose inhibited division protein A |
| 8 | 399 | InterPro | IPR040131 | MnmG, N-terminal domain |
| 9 | 28 | PRINTS | PR00368 | FAD-dependent pyridine nucleotide reductase signature |
| 148 | 166 | PRINTS | PR00368 | FAD-dependent pyridine nucleotide reductase signature |
| 567 | 620 | FunFam | G3DSA:1.10.150.570:FF:000001 | tRNA uridine 5-carboxymethylaminomethyl modification enzyme MnmG |
| 459 | 548 | FunFam | G3DSA:1.10.10.1800:FF:000001 | tRNA uridine 5-carboxymethylaminomethyl modification enzyme MnmG |
| 5 | 622 | Hamap | MF_00129 | tRNA uridine 5-carboxymethylaminomethyl modification enzyme MnmG [mnmG]. |
| 5 | 622 | InterPro | IPR004416 | tRNA uridine 5-carboxymethylaminomethyl modification enzyme MnmG |
| 7 | 261 | SUPERFAMILY | SSF51905 | FAD/NAD(P)-binding domain |
| 7 | 261 | InterPro | IPR036188 | FAD/NAD(P)-binding domain superfamily |
| 544 | 615 | SMART | SM01228 | GIDA_assoc_3_2 |
| 544 | 615 | InterPro | IPR047001 | tRNA uridine 5-carboxymethylaminomethyl modification enzyme, C-terminal subdomain |
| 402 | 614 | Pfam | PF13932 | tRNA modifying enzyme MnmG/GidA C-terminal domain |
| 402 | 614 | InterPro | IPR026904 | tRNA uridine 5-carboxymethylaminomethyl modification enzyme MnmG, C-terminal |
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...
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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
PA5565
|
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 | 0.442 |
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.
52 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 |
|---|---|---|---|---|---|---|
| GSH | Q5SID2 | 307.3 Da LogP -2.21 TPSA 158.8 | 1 viol. | ✓ Clean |
C(CC(=O)N[C@@H](CS)C(=O)NCC(=O)O)[C@@H](C(=O)O)N
|
|
| THG | Q5SID2 | 445.4 Da LogP -0.28 TPSA 211.6 | 1 viol. | ✓ Clean |
c1cc(ccc1C(=O)N[C@@H](CCC(=O)O)C(=O)O)NC[C@H]2C…
|
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 |
|---|---|---|---|---|---|
| ZINC3830891 | 1.000 | 307.3 Da LogP -2.21 TPSA 158.8 | 1 viol. | ✓ Clean |
N[C@@H](CCC(=O)N[C@@H](CS)C(=O)NCC(=O)O)C(=O)O
|
| ZINC3830892 | 1.000 | 307.3 Da LogP -2.21 TPSA 158.8 | 1 viol. | ✓ Clean |
N[C@@H](CCC(=O)N[C@H](CS)C(=O)NCC(=O)O)C(=O)O
|
| ZINC3830893 | 1.000 | 307.3 Da LogP -2.21 TPSA 158.8 | 1 viol. | ✓ Clean |
N[C@H](CCC(=O)N[C@@H](CS)C(=O)NCC(=O)O)C(=O)O
|
| ZINC3830894 | 1.000 | 307.3 Da LogP -2.21 TPSA 158.8 | 1 viol. | ✓ Clean |
N[C@H](CCC(=O)N[C@H](CS)C(=O)NCC(=O)O)C(=O)O
|
| ZINC4228235 | 1.000 | 445.4 Da LogP -0.28 TPSA 211.6 | 1 viol. | ✓ Clean |
Nc1nc2c(c(=O)[nH]1)N[C@H](CNc1ccc(C(=O)N[C@@H](…
|
| ZINC4228236 | 1.000 | 445.4 Da LogP -0.28 TPSA 211.6 | 1 viol. | ✓ Clean |
Nc1nc2c(c(=O)[nH]1)N[C@H](CNc1ccc(C(=O)N[C@H](C…
|
| ZINC4228237 | 1.000 | 445.4 Da LogP -0.28 TPSA 211.6 | 1 viol. | ✓ Clean |
Nc1nc2c(c(=O)[nH]1)N[C@@H](CNc1ccc(C(=O)N[C@@H]…
|
| ZINC4228238 | 1.000 | 445.4 Da LogP -0.28 TPSA 211.6 | 1 viol. | ✓ Clean |
Nc1nc2c(c(=O)[nH]1)N[C@@H](CNc1ccc(C(=O)N[C@H](…
|
| ZINC8618631 | 0.848 | 459.5 Da LogP 0.11 TPSA 211.6 | 1 viol. | ✓ Clean |
Nc1nc2c(c(=O)[nH]1)N[C@H](CCNc1ccc(C(=O)N[C@@H]…
|
| ZINC8627114 | 0.848 | 459.5 Da LogP 0.11 TPSA 211.6 | 1 viol. | ✓ Clean |
Nc1nc2c(c(=O)[nH]1)N[C@@H](CCNc1ccc(C(=O)N[C@@H…
|
| ZINC5828410 | 0.821 | 306.3 Da LogP -2.81 TPSA 164.6 | 1 viol. | ✓ Clean |
NC(=O)CNC(=O)[C@H](CS)NC(=O)CC[C@H](N)C(=O)O
|
| ZINC13549503 | 0.780 | 321.4 Da LogP -2.12 TPSA 147.8 | ✓ Ro5 | ✓ Clean |
COC(=O)[C@@H](N)CCC(=O)N[C@@H](CS)C(=O)NCC(=O)O
|
| ZINC4096455 | 0.775 | 321.4 Da LogP -1.82 TPSA 158.8 | 1 viol. | ✓ Clean |
N[C@@H](CCC(=O)N[C@@H](CS)C(=O)NCCC(=O)O)C(=O)O
|
| ZINC2554974 | 0.750 | 289.3 Da LogP -1.73 TPSA 158.8 | ✓ Ro5 | ✓ Clean |
CC[C@H](NC(=O)CC[C@H](N)C(=O)O)C(=O)NCC(=O)O
|
| ZINC3870040 | 0.750 | 250.3 Da LogP -1.32 TPSA 129.7 | ✓ Ro5 | ✓ Clean |
N[C@@H](CCC(=O)N[C@@H](CS)C(=O)O)C(=O)O
|
| ZINC3870041 | 0.750 | 250.3 Da LogP -1.32 TPSA 129.7 | ✓ Ro5 | ✓ Clean |
N[C@@H](CCC(=O)N[C@H](CS)C(=O)O)C(=O)O
|
| ZINC3870042 | 0.750 | 250.3 Da LogP -1.32 TPSA 129.7 | ✓ Ro5 | ✓ Clean |
N[C@H](CCC(=O)N[C@@H](CS)C(=O)O)C(=O)O
|
| ZINC3870043 | 0.750 | 250.3 Da LogP -1.32 TPSA 129.7 | ✓ Ro5 | ✓ Clean |
N[C@H](CCC(=O)N[C@H](CS)C(=O)O)C(=O)O
|
| ZINC3778474 | 0.727 | 349.4 Da LogP -1.34 TPSA 147.8 | ✓ Ro5 | ✓ Clean |
CC(C)OC(=O)CNC(=O)[C@H](CS)NC(=O)CC[C@H](N)C(=O…
|
| ZINC3778476 | 0.727 | 335.4 Da LogP -1.73 TPSA 147.8 | ✓ Ro5 | ✓ Clean |
CCOC(=O)CNC(=O)[C@H](CS)NC(=O)CC[C@H](N)C(=O)O
|
| ZINC5497203 | 0.727 | 335.4 Da LogP -1.73 TPSA 147.8 | ✓ Ro5 | ✓ Clean |
CCOC(=O)CNC(=O)[C@@H](CS)NC(=O)CC[C@H](N)C(=O)O
|
| ZINC5497237 | 0.727 | 335.4 Da LogP -1.73 TPSA 147.8 | ✓ Ro5 | ✓ Clean |
CCOC(=O)CNC(=O)[C@@H](CS)NC(=O)CC[C@@H](N)C(=O)O
|
| ZINC5497239 | 0.727 | 335.4 Da LogP -1.73 TPSA 147.8 | ✓ Ro5 | ✓ Clean |
CCOC(=O)CNC(=O)[C@H](CS)NC(=O)CC[C@@H](N)C(=O)O
|
| ZINC1532230 | 0.714 | 321.4 Da LogP -1.77 TPSA 158.8 | ✓ Ro5 | ✓ Clean |
CSC[C@H](NC(=O)CC[C@H](N)C(=O)O)C(=O)NCC(=O)O
|
| ZINC4556979 | 0.714 | 321.4 Da LogP -1.77 TPSA 158.8 | ✓ Ro5 | ✓ Clean |
CSC[C@@H](NC(=O)CC[C@H](N)C(=O)O)C(=O)NCC(=O)O
|
| ZINC4556980 | 0.714 | 321.4 Da LogP -1.77 TPSA 158.8 | ✓ Ro5 | ✓ Clean |
CSC[C@H](NC(=O)CC[C@@H](N)C(=O)O)C(=O)NCC(=O)O
|
| ZINC4556981 | 0.714 | 321.4 Da LogP -1.77 TPSA 158.8 | ✓ Ro5 | ✓ Clean |
CSC[C@@H](NC(=O)CC[C@@H](N)C(=O)O)C(=O)NCC(=O)O
|
| ZINC4228247 | 0.712 | 473.4 Da LogP -0.73 TPSA 219.8 | 1 viol. | ✓ Clean |
Nc1nc2c(c(=O)[nH]1)N[C@H](CN(C=O)c1ccc(C(=O)N[C…
|
| ZINC2005305 | 0.708 | 459.5 Da LogP -0.26 TPSA 202.8 | 1 viol. | ✓ Clean |
CN1c2c(nc(N)[nH]c2=O)NC[C@@H]1CNc1ccc(C(=O)N[C@…
|
| ZINC2572666 | 0.708 | 459.5 Da LogP -0.26 TPSA 202.8 | 1 viol. | ✓ Clean |
CN1c2c(nc(N)[nH]c2=O)NC[C@H]1CNc1ccc(C(=O)N[C@@…
|
| ZINC4228266 | 0.708 | 459.5 Da LogP -0.26 TPSA 202.8 | 1 viol. | ✓ Clean |
CN1c2c(nc(N)[nH]c2=O)NC[C@@H]1CNc1ccc(C(=O)N[C@…
|
| ZINC4228267 | 0.708 | 459.5 Da LogP -0.26 TPSA 202.8 | 1 viol. | ✓ Clean |
CN1c2c(nc(N)[nH]c2=O)NC[C@H]1CNc1ccc(C(=O)N[C@H…
|
| ZINC1616624 | 0.698 | 355.3 Da LogP -3.25 TPSA 213.2 | 1 viol. | ✓ Clean |
N[C@@H](CCC(=O)N[C@@H](CS(=O)(=O)O)C(=O)NCC(=O)…
|
| ZINC1616625 | 0.698 | 355.3 Da LogP -3.25 TPSA 213.2 | 1 viol. | ✓ Clean |
N[C@@H](CCC(=O)N[C@H](CS(=O)(=O)O)C(=O)NCC(=O)O…
|
| ZINC1616626 | 0.698 | 355.3 Da LogP -3.25 TPSA 213.2 | 1 viol. | ✓ Clean |
N[C@H](CCC(=O)N[C@@H](CS(=O)(=O)O)C(=O)NCC(=O)O…
|
| ZINC1616627 | 0.698 | 355.3 Da LogP -3.25 TPSA 213.2 | 1 viol. | ✓ Clean |
N[C@H](CCC(=O)N[C@H](CS(=O)(=O)O)C(=O)NCC(=O)O)…
|
| ZINC9212425 | 0.689 | 473.4 Da LogP -0.73 TPSA 219.8 | 1 viol. | ✓ Clean |
Nc1nc2c(c(=O)[nH]1)N(C=O)[C@@H](CNc1ccc(C(=O)N[…
|
| ZINC9212426 | 0.689 | 473.4 Da LogP -0.73 TPSA 219.8 | 1 viol. | ✓ Clean |
Nc1nc2c(c(=O)[nH]1)N(C=O)[C@H](CNc1ccc(C(=O)N[C…
|
| ZINC9212427 | 0.689 | 473.4 Da LogP -0.73 TPSA 219.8 | 1 viol. | ✓ Clean |
Nc1nc2c(c(=O)[nH]1)N(C=O)[C@@H](CNc1ccc(C(=O)N[…
|
| ZINC9212428 | 0.689 | 473.4 Da LogP -0.73 TPSA 219.8 | 1 viol. | ✓ Clean |
Nc1nc2c(c(=O)[nH]1)N(C=O)[C@H](CNc1ccc(C(=O)N[C…
|
| ZINC12496578 | 0.675 | 275.3 Da LogP -2.12 TPSA 158.8 | ✓ Ro5 | ✓ Clean |
C[C@H](NC(=O)CC[C@H](N)C(=O)O)C(=O)NCC(=O)O
|
| ZINC13522300 | 0.667 | 349.4 Da LogP -1.86 TPSA 175.9 | ✓ Ro5 | ✓ Clean |
CC(=O)SC[C@H](NC(=O)CC[C@H](N)C(=O)O)C(=O)NCC(=…
|
| ZINC31350707 | 0.667 | 349.4 Da LogP -1.86 TPSA 175.9 | ✓ Ro5 | ✓ Clean |
CC(=O)SC[C@@H](NC(=O)CC[C@@H](N)C(=O)O)C(=O)NCC…
|
| ZINC31350710 | 0.667 | 349.4 Da LogP -1.86 TPSA 175.9 | ✓ Ro5 | ✓ Clean |
CC(=O)SC[C@H](NC(=O)CC[C@@H](N)C(=O)O)C(=O)NCC(…
|
| ZINC3872732 | 0.667 | 336.3 Da LogP -1.72 TPSA 188.2 | ✓ Ro5 | ✓ Clean |
N[C@@H](CCC(=O)N[C@H](CSN=O)C(=O)NCC(=O)O)C(=O)O
|
| ZINC3872733 | 0.667 | 336.3 Da LogP -1.72 TPSA 188.2 | ✓ Ro5 | ✓ Clean |
N[C@H](CCC(=O)N[C@@H](CSN=O)C(=O)NCC(=O)O)C(=O)O
|
| ZINC3872734 | 0.667 | 336.3 Da LogP -1.72 TPSA 188.2 | ✓ Ro5 | ✓ Clean |
N[C@H](CCC(=O)N[C@H](CSN=O)C(=O)NCC(=O)O)C(=O)O
|
| ZINC4544082 | 0.667 | 335.4 Da LogP -1.38 TPSA 158.8 | ✓ Ro5 | ✓ Clean |
CCSC[C@H](NC(=O)CC[C@H](N)C(=O)O)C(=O)NCC(=O)O
|
| ZINC4544083 | 0.667 | 335.4 Da LogP -1.38 TPSA 158.8 | ✓ Ro5 | ✓ Clean |
CCSC[C@@H](NC(=O)CC[C@H](N)C(=O)O)C(=O)NCC(=O)O
|
| ZINC4544084 | 0.667 | 335.4 Da LogP -1.38 TPSA 158.8 | ✓ Ro5 | ✓ Clean |
CCSC[C@H](NC(=O)CC[C@@H](N)C(=O)O)C(=O)NCC(=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.