Protein profile

KP13_00821

tRNA-specific adenosine deaminase

Genome: KpKP13

Gene: tadA AHE43185.1 Structure source: AlphaFold + ColabFold UniProt A0A0H3GTS9
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Amino acids 172
Annotations 7
Features 14
PDB binders 14
Druggability 0.564

Overview

Basic information about this protein and its source genome.

Accession
KP13_00821
Assembly
Klebsiella pneumoniae subsp. pneumoniae Kp13, complete sequence
Gene
tadA AHE43185.1
Status
annotated
Amino acids
172
Structure source
AlphaFold + ColabFold
EC
3.5.4.33
GO
GO:0008270 Binding to a zinc ion (Zn). GO:0016787 Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. GO:0002100 The process in which an adenosine at position 34 of a tRNA is post-transcriptionally converted to inosine. The wobble nucleoside of the tRNA sequence (position 34) corresponds to the first position of the anticodon. 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. GO:0008251 Catalysis of the reaction: adenosine + H2O = inosine + NH4+, in a tRNA molecule. GO:0052717 Catalysis of the reaction: adenosine34 in tRNA + H2O + H+ = inosine34 in tRNA + NH4+.

Target profile

Computed evidence for target prioritization.

Human off-target
hit
Human identity (%)
48.387
Human E-value
5.17e-12
Gut microbiome off-target
hit
Essential (DEG)
Y
DEG identity (%)
84.337
DEG E-value
1.2000000000000001e-106
Localization
Cytoplasmic
ColabFold pLDDT
94.84

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 0.564
Structure A0A0H3GTS9
Pocket Pocket 2
P2Rank 0.502
Structure A0A0H3GTS9
Pocket Pocket 1
ColabFold model
FPocket 0.626 · Pocket 5
P2Rank 0.489 · Pocket 1
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 321 / 4744 genomes with a hit
Normalized 0.068

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)

1

Gene Ontology (GO)

6
  • GO:0008270 Binding to a zinc ion (Zn).
  • GO:0016787 Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc.
  • GO:0002100 The process in which an adenosine at position 34 of a tRNA is post-transcriptionally converted to inosine. The wobble nucleoside of the tRNA sequence (position 34) corresponds to the first position of the anticodon.
  • 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.
  • GO:0008251 Catalysis of the reaction: adenosine + H2O = inosine + NH4+, in a tRNA molecule.
  • GO:0052717 Catalysis of the reaction: adenosine34 in tRNA + H2O + H+ = inosine34 in tRNA + NH4+.

Sequence Features

Domain/signature hits from InterPro and related databases.

14 records
Show feature table
Start End DB Term Name
4 167 FunFam G3DSA:3.40.140.10:FF:000005 tRNA-specific adenosine deaminase
4 170 Gene3D G3DSA:3.40.140.10 Cytidine Deaminase, domain 2
10 160 SUPERFAMILY SSF53927 Cytidine deaminase-like
10 160 InterPro IPR016193 Cytidine deaminase-like
60 97 ProSitePatterns PS00903 Cytidine and deoxycytidylate deaminases zinc-binding region signature.
60 97 InterPro IPR016192 APOBEC/CMP deaminase, zinc-binding
8 159 PANTHER PTHR11079 CYTOSINE DEAMINASE FAMILY MEMBER
10 156 Pfam PF14437 MafB19-like deaminase
10 156 InterPro IPR028883 tRNA-specific adenosine deaminase
9 120 ProSiteProfiles PS51747 Cytidine and deoxycytidylate deaminases domain profile.
9 120 InterPro IPR002125 Cytidine and deoxycytidylate deaminase domain
15 120 CDD cd01285 nucleoside_deaminase
15 156 Hamap MF_00972 tRNA-specific adenosine deaminase [tadA].
15 156 InterPro IPR028883 tRNA-specific adenosine deaminase

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_A0A0H3GTS9
AlphaFold — — full sequence — Viewing
ColabFold KP13_00821
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
2 0.564
1 0.16
3 0.032
8 0.007

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 10.88 0.502
2 1.78 0.028

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.

64 records

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.

Show only:
Ligand Source crystal UniProt (homolog) MW · LogP · TPSA Lipinski PAINS SMILES
5AZ
5XKP
A0QY90 112.1 Da LogP -1.25 TPSA 84.7 ✓ Ro5 ✓ Clean C1=NC(=O)NC(=N1)N
5GP
3ZPG
D0CB74 363.2 Da LogP -2.57 TPSA 206.0 1 viol. ✓ Clean c1nc2c(n1[C@H]3[C@@H]([C@@H]([C@H](O3)COP(=O)(O…
6AM
5XKQ
A0QY90 127.1 Da LogP -1.26 TPSA 110.9 ✓ Ro5 ✓ Clean c1(nc(nc(n1)O)N)N
AI9
4G3M
P17618 354.2 Da LogP -3.46 TPSA 231.5 1 viol. ✓ Clean C([C@H]([C@H]([C@H](/C=N/C1=C(C(=O)NC(=O)N1)N)O…
AIF
3EX8
P17618 354.2 Da LogP -3.46 TPSA 231.5 1 viol. ✓ Clean C([C@H]([C@H]([C@@H](\C=N\C1=C(C(=O)NC(=O)N1)N)…
AOF
4G3M
P17618 354.2 Da LogP -3.39 TPSA 220.2 1 viol. ✓ Clean C([C@@H]1[C@H]([C@H]([C@@H](O1)NC2=C(C(=O)NC(=O…
BZE
5XKR
A0QY90 187.2 Da LogP 0.70 TPSA 90.7 ✓ Ro5 ✓ Clean c1ccc(cc1)c2nc(nc(n2)N)N
CAC
5XKO
A0QY90 137.0 Da LogP -0.52 TPSA 40.1 ✓ Ro5 ✓ Clean C[As](=O)(C)[O-]
DCP
2HVW
Q8DSE5 467.2 Da LogP -1.18 TPSA 250.2 2 viol. ✓ Clean C1[C@@H]([C@H](O[C@H]1N2C=CC(=NC2=O)N)CO[P@@](=…
DDN
2HVW
Q8DSE5 310.2 Da LogP -1.57 TPSA 148.8 ✓ Ro5 ✓ Clean C1[C@@H]([C@H](O[C@H]1N2C=C[C@H](NC2=O)O)COP(=O…
DUC
1UAQ
Q12178 114.1 Da LogP -0.78 TPSA 58.2 ✓ Ro5 ✓ Clean C1CNC(=O)NC1=O
HPY
1P6O
Q12178 114.1 Da LogP -0.87 TPSA 61.4 ✓ Ro5 ✓ Clean C1=CNC(=O)N[C@H]1O
OXL
3ZPG
D0CB74 88.0 Da LogP -3.51 TPSA 80.3 ✓ Ro5 ✓ Clean C(=O)(C(=O)[O-])[O-]
TTP
5C2O
Q8DSE5 482.2 Da LogP -1.16 TPSA 244.1 2 viol. ✓ Clean CC1=CN(C(=O)NC1=O)[C@H]2C[C@@H]([C@H](O2)CO[P@]…

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.