Protein profile

KP13_04822

2,3-dihydroxybenzoate-AMP ligase

Genome: KpKP13

Gene: AHE43789.1 dhbE Structure source: AlphaFold + ColabFold UniProt A0A0H3GSA9
Amino acids 525
Annotations 1
Features 18
PDB binders 7
Druggability 0.932

Overview

Basic information about this protein and its source genome.

Accession
KP13_04822
Gene
AHE43789.1 dhbE
Status
annotated
Amino acids
525
Structure source
AlphaFold + ColabFold

Target profile

Computed evidence for target prioritization.

Human off-target
hit
Human identity (%)
36.709
Human E-value
8.02e-18
Gut microbiome off-target
hit
Essential (DEG)
Y
DEG identity (%)
44.93
DEG E-value
1.63e-132
Localization
CytoplasmicMembrane
ColabFold pLDDT
91.5

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 0.932
Structure A0A0H3GSA9
Pocket Pocket 1
P2Rank 0.983
Structure A0A0H3GSA9
Pocket Pocket 1
ColabFold model
FPocket 0.543 · Pocket 7
P2Rank 0.948 · Pocket 1
Core conservation Accessory gene
Roary accessory
CoreCruncher accessory
Gut microbiome 14 / 4744 genomes with a hit
Normalized 0.003

Sequence

Primary amino-acid sequence viewer.

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 GO

Gene Ontology (GO)

1
  • GO:0016878 Catalysis of the joining of an acid and a thiol via a carbon-sulfur bond, with the concomitant hydrolysis of the diphosphate bond in ATP or a similar triphosphate.

Sequence Features

Domain/signature hits from InterPro and related databases.

18 records
Show feature table
Start End DB Term Name
169 340 Gene3D G3DSA:3.40.50.980 -
13 166 FunFam G3DSA:3.40.50.980:FF:000004 2,3-dihydroxybenzoate-AMP ligase
10 518 SUPERFAMILY SSF56801 Acetyl-CoA synthetase-like
21 422 Pfam PF00501 AMP-binding enzyme
21 422 InterPro IPR000873 AMP-dependent synthetase/ligase domain
10 517 PANTHER PTHR43767 LONG-CHAIN-FATTY-ACID--COA LIGASE
174 185 ProSitePatterns PS00455 Putative AMP-binding domain signature.
174 185 InterPro IPR020845 AMP-binding, conserved site
4 512 CDD cd05920 23DHB-AMP_lg
341 415 Gene3D G3DSA:2.30.38.10 Luciferase; Domain 3
431 506 Pfam PF13193 AMP-binding enzyme C-terminal domain
431 506 InterPro IPR025110 AMP-binding enzyme, C-terminal domain
341 415 FunFam G3DSA:2.30.38.10:FF:000003 Vibriobactin-specific 2,3-dihydroxybenzoate-AMP ligase
417 522 Gene3D G3DSA:3.30.300.30 -
417 522 InterPro IPR045851 AMP-binding enzyme, C-terminal domain superfamily
417 520 FunFam G3DSA:3.30.300.30:FF:000008 2,3-dihydroxybenzoate-AMP ligase
15 166 Gene3D G3DSA:3.40.50.980 -
168 340 FunFam G3DSA:3.40.50.980:FF:000003 Vibriobactin-specific 2,3-dihydroxybenzoate-AMP ligase

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_A0A0H3GSA9
AlphaFold full sequence Viewing
ColabFold KP13_04822
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
1 0.932

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 28.83 0.928
2 8.86 0.474
3 2.18 0.052
4 2.03 0.045
5 1.44 0.019

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.

139 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
B5M A0A140DJY3 481.4 Da LogP 0.02 TPSA 212.4 1 viol. ✓ Clean Cc1cccc(c1C(=O)OP(=O)(O)OC[C@H]2[C@H]([C@H]([C@…
B5V A0A140DJY3 467.3 Da LogP -0.29 TPSA 212.4 1 viol. ✓ Clean c1ccc(c(c1)C(=O)OP(=O)(O)OC[C@H]2[C@H]([C@H]([C…
B5Y A0A140DJY3 481.4 Da LogP 0.02 TPSA 212.4 1 viol. ✓ Clean Cc1ccc(c(c1)C(=O)OP(=O)(O)OC[C@H]2[C@H]([C@H]([…
DBH P40871 154.1 Da LogP 0.80 TPSA 77.8 ✓ Ro5 Alert c1cc(c(c(c1)O)O)C(=O)O
J2J Q47NR5 483.3 Da LogP -0.59 TPSA 232.6 2 viol. Alert c1cc(c(c(c1)O)O)C(=O)OP(=O)(O)OC[C@@H]2[C@H]([C…
OOB A0A140DJY3 451.3 Da LogP 0.00 TPSA 192.1 1 viol. ✓ Clean c1ccc(cc1)C(=O)OP(=O)(O)OC[C@@H]2[C@H]([C@H]([C…
SAL A0A140DJY3 138.1 Da LogP 1.09 TPSA 57.5 ✓ Ro5 ✓ Clean c1ccc(c(c1)C(=O)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.