Protein profile

VK055_3513

envC murein hydrolase

Genome: KpATCC43816

Gene: yibP AIK82069.1 Structure source: AlphaFold + ColabFold UniProt A0A0H3GUR0
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Amino acids 418
Annotations 1
Features 25
PDB binders 3
Druggability 0.621

Overview

Basic information about this protein and its source genome.

Accession
VK055_3513
Assembly
Klebsiella pneumoniae subsp. pneumoniae strain ATCC 43816 KPPR1, complete genome
Gene
yibP AIK82069.1
Status
annotated
Amino acids
418
Structure source
AlphaFold + ColabFold
GO
GO:0004222 Catalysis of the hydrolysis of internal, alpha-peptide bonds in a polypeptide chain by a mechanism in which water acts as a nucleophile, one or two metal ions hold the water molecule in place, and charged amino acid side chains are ligands for the metal ions.

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 (%)
56.429
DEG E-value
1.14e-155
Localization
OuterMembrane
ColabFold pLDDT
86.76

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 0.621
Structure A0A0H3GUR0
Pocket Pocket 10
P2Rank 0.786
Structure A0A0H3GUR0
Pocket Pocket 1
ColabFold model
FPocket 0.779 · Pocket 13
P2Rank 0.776 · Pocket 1
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 111 / 4744 genomes with a hit
Normalized 0.023

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:0004222 Catalysis of the hydrolysis of internal, alpha-peptide bonds in a polypeptide chain by a mechanism in which water acts as a nucleophile, one or two metal ions hold the water molecule in place, and charged amino acid side chains are ligands for the metal ions.

Sequence Features

Domain/signature hits from InterPro and related databases.

25 records
Show feature table
Start End DB Term Name
319 412 Pfam PF01551 Peptidase family M23
319 412 InterPro IPR016047 Peptidase M23
17 28 Phobius SIGNAL_PEPTIDE_H_REGION Hydrophobic region of a signal peptide.
246 276 MobiDBLite mobidb-lite consensus disorder prediction
44 417 PANTHER PTHR21666 PEPTIDASE-RELATED
39 122 Coils Coil Coil
277 418 Gene3D G3DSA:2.70.70.10 Glucose Permease (Domain IIA)
277 418 InterPro IPR011055 Duplicated hybrid motif
218 416 SUPERFAMILY SSF51261 Duplicated hybrid motif
218 416 InterPro IPR011055 Duplicated hybrid motif
246 286 MobiDBLite mobidb-lite consensus disorder prediction
1 33 SignalP_EUK SignalP-noTM SignalP-noTM
162 185 Coils Coil Coil
1 33 SignalP_GRAM_POSITIVE SignalP-TM SignalP-TM
211 245 Coils Coil Coil
1 16 Phobius SIGNAL_PEPTIDE_N_REGION N-terminal region of a signal peptide.
34 418 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
57 271 Gene3D G3DSA:6.10.250.3150 -
320 403 CDD cd12797 M23_peptidase
283 418 FunFam G3DSA:2.70.70.10:FF:000003 Murein hydrolase activator EnvC
247 267 Coils Coil Coil
1 33 Phobius SIGNAL_PEPTIDE Signal peptide region
29 33 Phobius SIGNAL_PEPTIDE_C_REGION C-terminal region of a signal peptide.
206 230 MobiDBLite mobidb-lite consensus disorder prediction
212 230 MobiDBLite mobidb-lite consensus disorder prediction

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_A0A0H3GUR0
AlphaFold — — full sequence — Viewing
ColabFold VK055_3513
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
10 0.621
1 0.031
11 0.002
18 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 20.0 0.786
2 4.24 0.143
3 1.35 0.013

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.

22 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
4SQ
4ZYB
O33599 281.2 Da LogP -2.12 TPSA 158.8 ✓ Ro5 ✓ Clean C(CP(=O)(CNC(=O)CN)O)C(=O)NCC(=O)O
CAC
2B0P
O33599 137.0 Da LogP -0.52 TPSA 40.1 ✓ Ro5 ✓ Clean C[As](=O)(C)[O-]
TLA
2B13
O33599 150.1 Da LogP -2.12 TPSA 115.1 ✓ Ro5 ✓ Clean [C@@H]([C@H](C(=O)O)O)(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.