Protein profile

KP13_00549

tRNA (uracil-5-)-methyltransferase

Genome: KpKP13

Gene: AHE47025.1 trmA Structure source: AlphaFold + ColabFold UniProt A0A0H3GGE9
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Amino acids 366
Annotations 8
Features 22
PDB binders 0
Druggability 0.411

Overview

Basic information about this protein and its source genome.

Accession
KP13_00549
Assembly
Klebsiella pneumoniae subsp. pneumoniae Kp13, complete sequence
Gene
AHE47025.1 trmA
Status
annotated
Amino acids
366
Structure source
AlphaFold + ColabFold
EC
2.1.1.35
GO
GO:0008173 Catalysis of the transfer of a methyl group from a donor to a nucleoside residue in an RNA molecule. GO:0030697 Catalysis of the reaction: S-adenosyl-L-methionine + uridine54 in tRNA = 5-methyluridine54 in tRNA + H+ + S-adenosyl-L-homocysteine. GO:0006396 Any process involved in the conversion of one or more primary RNA transcripts into one or more mature RNA molecules. GO:0005829 The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes. GO:0019843 Binding to a ribosomal RNA. GO:0000049 Binding to a transfer RNA.

Target profile

Computed evidence for target prioritization.

Human off-target
hit
Human identity (%)
29.213
Human E-value
1.7e-10
Gut microbiome off-target
hit
Essential (DEG)
N
DEG identity (%)
0.0
Localization
Cytoplasmic
ColabFold pLDDT
96.81

Selected Druggability evidence

AlphaFold / UniProt model

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 0.411
Structure A0A0H3GGE9
Pocket Pocket 9
P2Rank 0.54
Structure A0A0H3GGE9
Pocket Pocket 1
ColabFold model
FPocket 0.55 · Pocket 10
P2Rank 0.745 · Pocket 1
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 175 / 4744 genomes with a hit
Normalized 0.037

Sequence

Primary amino-acid sequence viewer.

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 7 GO

Enzyme Commission (EC)

1

Gene Ontology (GO)

7
  • GO:0008173 Catalysis of the transfer of a methyl group from a donor to a nucleoside residue in an RNA molecule.
  • GO:0030697 Catalysis of the reaction: S-adenosyl-L-methionine + uridine54 in tRNA = 5-methyluridine54 in tRNA + H+ + S-adenosyl-L-homocysteine.
  • GO:0006396 Any process involved in the conversion of one or more primary RNA transcripts into one or more mature RNA molecules.
  • GO:0005829 The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
  • GO:0019843 Binding to a ribosomal RNA.
  • GO:0000049 Binding to a transfer RNA.
  • GO:0030488 The posttranscriptional addition of methyl groups to specific residues in a tRNA molecule.

Sequence Features

Domain/signature hits from InterPro and related databases.

22 records
Show feature table
Start End DB Term Name
4 366 Hamap MF_01011 tRNA/tmRNA (uracil-C(5))-methyltransferase [trmA].
4 366 InterPro IPR011869 tRNA/tmRNA (uracil-C(5))-methyltransferase, TrmA
348 358 ProSitePatterns PS01231 RNA methyltransferase trmA family signature 2.
348 358 InterPro IPR030391 RNA methyltransferase TrmA, conserved site
6 365 SUPERFAMILY SSF53335 S-adenosyl-L-methionine-dependent methyltransferases
6 365 InterPro IPR029063 S-adenosyl-L-methionine-dependent methyltransferase superfamily
10 366 Pfam PF05958 tRNA (Uracil-5-)-methyltransferase
10 366 InterPro IPR010280 (Uracil-5)-methyltransferase family
299 328 ProSitePatterns PS01230 RNA methyltransferase trmA family signature 1.
299 328 InterPro IPR030390 RNA methyltransferase TrmA, active site
1 366 PANTHER PTHR47790 TRNA/TMRNA (URACIL-C(5))-METHYLTRANSFERASE
1 366 InterPro IPR011869 tRNA/tmRNA (uracil-C(5))-methyltransferase, TrmA
175 362 FunFam G3DSA:3.40.50.150:FF:000012 tRNA/tmRNA (uracil-C(5))-methyltransferase
15 362 Gene3D G3DSA:3.40.50.150 Vaccinia Virus protein VP39
15 362 InterPro IPR029063 S-adenosyl-L-methionine-dependent methyltransferase superfamily
45 189 Gene3D G3DSA:2.40.50.1070 -
2 366 ProSiteProfiles PS51687 SAM-dependent methyltransferase RNA m(5)U-type domain profile.
2 366 InterPro IPR010280 (Uracil-5)-methyltransferase family
10 366 NCBIfam TIGR02143 tRNA (uridine(54)-C5)-methyltransferase TrmA
10 366 InterPro IPR011869 tRNA/tmRNA (uracil-C(5))-methyltransferase, TrmA
213 320 CDD cd02440 AdoMet_MTases
45 189 FunFam G3DSA:2.40.50.1070:FF:000001 tRNA/tmRNA (uracil-C(5))-methyltransferase

3D Structure

Selected loaded structure. Experimental PDB entries may cover only a portion of the sequence; predicted models typically cover the full protein.

3D visualization script Full viewer

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Structural evidence

0 + 2

Experimental PDB entries and predicted models. Click Switch to display a different structure in the viewer.

Entry Method Resolution Chain Coverage Links Status
AlphaFold AF_A0A0H3GGE9
AlphaFold — — full sequence — Viewing
ColabFold KP13_00549
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
9 0.411

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 8.67 0.464
2 8.61 0.46
3 3.45 0.125

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.

50 records

Proposed virtual-screening candidates from ZINC. Score = Tanimoto similarity to a known binder (0–1; higher = more similar).

Show only:
Ligand Tanimoto MW · LogP · TPSA Lipinski PAINS SMILES
ZINC12501520 1.000 458.5 Da LogP -0.88 TPSA 123.5 1 viol. ✓ Clean OCCOCCOCCOCCOCCOCCOCCOCCOCCOCCO
ZINC3874716 1.000 414.5 Da LogP -0.90 TPSA 114.3 ✓ Ro5 ✓ Clean OCCOCCOCCOCCOCCOCCOCCOCCOCCO
ZINC4283769 1.000 238.3 Da LogP -0.96 TPSA 77.4 ✓ Ro5 ✓ Clean OCCOCCOCCOCCOCCO
ZINC4521548 1.000 282.3 Da LogP -0.95 TPSA 86.6 ✓ Ro5 ✓ Clean OCCOCCOCCOCCOCCOCCO
ZINC5178829 1.000 326.4 Da LogP -0.93 TPSA 95.8 ✓ Ro5 ✓ Clean OCCOCCOCCOCCOCCOCCOCCO
ZINC5178830 1.000 370.4 Da LogP -0.91 TPSA 105.1 ✓ Ro5 ✓ Clean OCCOCCOCCOCCOCCOCCOCCOCCO
ZINC115086873 0.688 209.2 Da LogP -1.08 TPSA 83.2 ✓ Ro5 ✓ Clean NOCCOCCOCCOCCO
ZINC137432264 0.688 457.6 Da LogP -0.91 TPSA 129.3 1 viol. ✓ Clean NCCOCCOCCOCCOCCOCCOCCOCCOCCOCCO
ZINC146143823 0.688 237.3 Da LogP -1.00 TPSA 83.2 ✓ Ro5 ✓ Clean NCCOCCOCCOCCOCCO
ZINC1542984442 0.688 413.5 Da LogP -0.93 TPSA 120.1 ✓ Ro5 ✓ Clean NCCOCCOCCOCCOCCOCCOCCOCCOCCO
ZINC1565503710 0.688 254.3 Da LogP -0.03 TPSA 57.2 ✓ Ro5 ✓ Clean OCCOCCOCCOCCOCCS
ZINC1580161 0.688 208.3 Da LogP -0.33 TPSA 57.2 ✓ Ro5 ✓ Clean COCCOCCOCCOCCO
ZINC16052118 0.688 340.4 Da LogP -0.28 TPSA 84.8 ✓ Ro5 ✓ Clean COCCOCCOCCOCCOCCOCCOCCO
ZINC16052257 0.688 384.5 Da LogP -0.26 TPSA 94.1 ✓ Ro5 ✓ Clean COCCOCCOCCOCCOCCOCCOCCOCCO
ZINC1857792028 0.688 430.6 Da LogP 0.04 TPSA 94.1 ✓ Ro5 ✓ Clean OCCOCCOCCOCCOCCOCCOCCOCCOCCS
ZINC1857792057 0.688 474.6 Da LogP 0.06 TPSA 103.3 1 viol. ✓ Clean OCCOCCOCCOCCOCCOCCOCCOCCOCCOCCS
ZINC230494776 0.688 325.4 Da LogP -0.96 TPSA 101.6 ✓ Ro5 ✓ Clean NCCOCCOCCOCCOCCOCCOCCO
ZINC34317654 0.688 472.6 Da LogP -0.23 TPSA 112.5 1 viol. ✓ Clean COCCOCCOCCOCCOCCOCCOCCOCCOCCOCCO
ZINC38917157 0.688 210.3 Da LogP -0.04 TPSA 47.9 ✓ Ro5 ✓ Clean OCCOCCOCCOCCS
ZINC44076059 0.688 428.5 Da LogP -0.24 TPSA 103.3 ✓ Ro5 ✓ Clean COCCOCCOCCOCCOCCOCCOCCOCCOCCO
ZINC5210101 0.688 252.3 Da LogP -0.31 TPSA 66.4 ✓ Ro5 ✓ Clean COCCOCCOCCOCCOCCO
ZINC5650743 0.688 222.3 Da LogP 0.07 TPSA 57.2 ✓ Ro5 ✓ Clean CCOCCOCCOCCOCCO
ZINC5997860 0.688 296.4 Da LogP -0.29 TPSA 75.6 ✓ Ro5 ✓ Clean COCCOCCOCCOCCOCCOCCO
ZINC6403917 0.688 354.4 Da LogP 0.11 TPSA 84.8 ✓ Ro5 ✓ Clean CCOCCOCCOCCOCCOCCOCCOCCO
ZINC77271182 0.688 281.3 Da LogP -0.98 TPSA 92.4 ✓ Ro5 ✓ Clean NCCOCCOCCOCCOCCOCCO
ZINC83253921 0.688 369.5 Da LogP -0.95 TPSA 110.9 ✓ Ro5 ✓ Clean NCCOCCOCCOCCOCCOCCOCCOCCO
ZINC90741446 0.688 386.5 Da LogP 0.02 TPSA 84.8 ✓ Ro5 ✓ Clean OCCOCCOCCOCCOCCOCCOCCOCCS
ZINC90741447 0.688 298.4 Da LogP -0.01 TPSA 66.4 ✓ Ro5 ✓ Clean OCCOCCOCCOCCOCCOCCS
ZINC144169243 0.647 281.3 Da LogP -1.37 TPSA 89.4 ✓ Ro5 ✓ Clean OCCOCCOCCNCCOCCOCCO
ZINC205758716 0.647 457.6 Da LogP -1.31 TPSA 126.3 1 viol. ✓ Clean OCCOCCOCCOCCOCCNCCOCCOCCOCCOCCO
ZINC575441396 0.647 369.5 Da LogP -1.34 TPSA 107.9 ✓ Ro5 ✓ Clean OCCOCCOCCOCCNCCOCCOCCOCCO
ZINC1644613 0.611 206.3 Da LogP 0.83 TPSA 47.9 ✓ Ro5 ✓ Clean CCCCOCCOCCOCCO
ZINC258839852 0.611 276.3 Da LogP 0.61 TPSA 57.2 ✓ Ro5 ✓ Clean OCCOCCOCCOCCOCC(F)(F)F
ZINC167715346 0.600 266.3 Da LogP -0.18 TPSA 77.4 ✓ Ro5 ✓ Clean OCCCOCCOCCOCCOCCCO
ZINC34160867 0.600 222.3 Da LogP -0.20 TPSA 68.2 ✓ Ro5 ✓ Clean OCCCOCCOCCOCCCO
ZINC1580159 0.588 210.3 Da LogP -0.26 TPSA 58.9 ✓ Ro5 ✓ Clean OCCOCCSCCOCCO
ZINC142610155 0.579 340.4 Da LogP -0.84 TPSA 112.9 ✓ Ro5 ✓ Clean O=C(O)COCCOCCOCCOCCOCCOCCO
ZINC1542984426 0.579 428.5 Da LogP -0.80 TPSA 131.4 ✓ Ro5 ✓ Clean O=C(O)COCCOCCOCCOCCOCCOCCOCCOCCO
ZINC1542984432 0.579 398.4 Da LogP -0.43 TPSA 122.1 ✓ Ro5 ✓ Clean O=C(O)CCOCCOCCOCCOCCOCCOCCOCCO
ZINC207588231 0.579 207.3 Da LogP -0.75 TPSA 60.0 ✓ Ro5 ✓ Clean CNCCOCCOCCOCCO
ZINC258828116 0.579 452.5 Da LogP -0.24 TPSA 103.3 ✓ Ro5 ✓ Clean C#CCOCCOCCOCCOCCOCCOCCOCCOCCOCCO
ZINC258836919 0.579 364.4 Da LogP -0.27 TPSA 84.8 ✓ Ro5 ✓ Clean C#CCOCCOCCOCCOCCOCCOCCOCCO
ZINC33967025 0.579 252.3 Da LogP -0.87 TPSA 94.5 ✓ Ro5 ✓ Clean O=C(O)COCCOCCOCCOCCO
ZINC39267847 0.579 208.2 Da LogP -0.89 TPSA 85.2 ✓ Ro5 ✓ Clean O=C(O)COCCOCCOCCO
ZINC575440725 0.579 295.4 Da LogP -1.03 TPSA 80.6 ✓ Ro5 ✓ Clean CN(CCOCCOCCO)CCOCCOCCO
ZINC83254087 0.579 266.3 Da LogP -0.48 TPSA 94.5 ✓ Ro5 ✓ Clean O=C(O)CCOCCOCCOCCOCCO
ZINC95920522 0.579 296.3 Da LogP -0.85 TPSA 103.7 ✓ Ro5 ✓ Clean O=C(O)COCCOCCOCCOCCOCCO
ZINC96503406 0.579 276.3 Da LogP -0.31 TPSA 66.4 ✓ Ro5 ✓ Clean C#CCOCCOCCOCCOCCOCCO
ZINC96503425 0.579 222.2 Da LogP -0.50 TPSA 85.2 ✓ Ro5 ✓ Clean O=C(O)CCOCCOCCOCCO
ZINC96503526 0.579 442.5 Da LogP -0.41 TPSA 131.4 ✓ Ro5 ✓ Clean O=C(O)CCOCCOCCOCCOCCOCCOCCOCCOCCO

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.