Protein profile

VK055_1153

amidohydrolase family protein

Genome: KpATCC43816

Gene: AIK79776.1 Structure source: AlphaFold + ColabFold UniProt A0A0H3GW81
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Amino acids 381
Annotations 4
Features 17
PDB binders 3
Druggability 0.35

Overview

Basic information about this protein and its source genome.

Accession
VK055_1153
Assembly
Klebsiella pneumoniae subsp. pneumoniae strain ATCC 43816 KPPR1, complete genome
Gene
AIK79776.1
Status
annotated
Amino acids
381
Structure source
AlphaFold + ColabFold
GO
GO:0016787 Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. GO:0046872 Binding to a metal ion. GO:0050118 Catalysis of the reaction: H2O + N-acetyl-(2S,6S)-2,6-diaminoheptanedioate = (2S,6S)-2,6-diaminoheptanedioate + acetate. GO:0019877 OBSOLETE. The chemical reactions and pathways resulting in the formation of diaminopimelate, both as an intermediate in lysine biosynthesis and as a component (as meso-diaminopimelate) of the peptidoglycan of Gram-negative bacterial cell walls.

Target profile

Computed evidence for target prioritization.

Human off-target
No hit
Human identity (%)
0.0
Gut microbiome off-target
hit
Essential (DEG)
Y
DEG identity (%)
52.66
DEG E-value
4.0800000000000005e-132
Localization
Cytoplasmic
ColabFold pLDDT
97.57

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 0.35
Structure A0A0H3GW81
Pocket Pocket 8
P2Rank 0.544
Structure A0A0H3GW81
Pocket Pocket 1
ColabFold model
FPocket 0.207 · Pocket 11
P2Rank 0.683 · Pocket 1
Core conservation Accessory gene
Roary core
CoreCruncher accessory
Gut microbiome 45 / 4744 genomes with a hit
Normalized 0.009

Sequence

Primary amino-acid sequence viewer.

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

4 GO

Gene Ontology (GO)

4
  • GO:0016787 Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc.
  • GO:0046872 Binding to a metal ion.
  • GO:0050118 Catalysis of the reaction: H2O + N-acetyl-(2S,6S)-2,6-diaminoheptanedioate = (2S,6S)-2,6-diaminoheptanedioate + acetate.
  • GO:0019877 OBSOLETE. The chemical reactions and pathways resulting in the formation of diaminopimelate, both as an intermediate in lysine biosynthesis and as a component (as meso-diaminopimelate) of the peptidoglycan of Gram-negative bacterial cell walls.

Sequence Features

Domain/signature hits from InterPro and related databases.

17 records
Show feature table
Start End DB Term Name
1 381 PIRSF PIRSF005962 Amidohydrol_AmhX
1 381 InterPro IPR017439 Amidohydrolase
7 380 PANTHER PTHR11014 PEPTIDASE M20 FAMILY MEMBER
7 380 InterPro IPR017439 Amidohydrolase
9 367 NCBIfam TIGR01891 amidohydrolase
9 367 InterPro IPR017439 Amidohydrolase
9 365 Gene3D G3DSA:3.40.630.10 Zn peptidases
6 378 CDD cd05666 M20_Acy1-like
67 376 Pfam PF01546 Peptidase family M20/M25/M40
67 376 InterPro IPR002933 Peptidase M20
179 275 Pfam PF07687 Peptidase dimerisation domain
179 275 InterPro IPR011650 Peptidase M20, dimerisation domain
5 380 SUPERFAMILY SSF53187 Zn-dependent exopeptidases
175 289 Gene3D G3DSA:3.30.70.360 -
175 292 FunFam G3DSA:3.30.70.360:FF:000001 N-acetyldiaminopimelate deacetylase
177 283 SUPERFAMILY SSF55031 Bacterial exopeptidase dimerisation domain
177 283 InterPro IPR036264 Bacterial exopeptidase dimerisation domain

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

Loading 3D structure...

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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_A0A0H3GW81
AlphaFold — — full sequence — Viewing
ColabFold VK055_1153
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 0.014
7 0.013
1 0.004
13 0.0

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 11.87 0.544
2 1.34 0.013
3 0.97 0.005

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.

53 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
BTB
6SLF
Q8GGD4 209.2 Da LogP -3.01 TPSA 104.4 ✓ Ro5 ✓ Clean C(CO)N(CCO)C(CO)(CO)CO
LJ8
6SLF
Q8GGD4 369.4 Da LogP 2.88 TPSA 117.7 ✓ Ro5 ✓ Clean C[C@@H](CCc1ccccc1)CCP(=O)(C[C@@H](CCC(=O)N)C(=…
PE7
4EWT
A0A0H2WZV8 342.5 Da LogP 0.01 TPSA 75.6 ✓ Ro5 ✓ Clean C(COCCOCCOCCOCCOCCOCCS)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.