Protein profile

VK055_0674

coenzyme PQQ biosynthesis protein PqqF

Genome: KpATCC43816

Gene: pqqF AIK79298.1 Structure source: AlphaFold + ColabFold UniProt A0A4S4WK18
Amino acids 761
Annotations 5
Features 13
PDB binders 34
Druggability 0.303

Overview

Basic information about this protein and its source genome.

Accession
VK055_0674
Gene
pqqF AIK79298.1
Status
annotated
Amino acids
761
Structure source
AlphaFold + ColabFold

Target profile

Computed evidence for target prioritization.

Human off-target
hit
Human identity (%)
24.928
Human E-value
1.11e-20
Gut microbiome off-target
hit
Essential (DEG)
N
DEG identity (%)
0.0
Localization
Periplasmic
ColabFold pLDDT
91.93

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 0.303
Structure A0A4S4WK18
Pocket Pocket 19
P2Rank 0.504
Structure A0A4S4WK18
Pocket Pocket 1
ColabFold model
FPocket 0.328 · Pocket 9
P2Rank 0.762 · Pocket 1
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 7 / 4744 genomes with a hit
Normalized 0.001

Sequence

Primary amino-acid sequence viewer.

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

5 GO

Gene Ontology (GO)

5
  • GO:0006508 The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.
  • GO:0018189 The chemical reactions and pathways resulting in the formation of the cofactor pyrroloquinoline quinone (PQQ); it is synthesized from a small peptide containing tyrosine and glutamic acid; these amino acids in the peptide are multiply cross-linked and the rest of the peptide is removed.
  • GO:0046872 Binding to a metal ion.
  • GO:0008270 Binding to a zinc ion (Zn).
  • 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.

13 records
Show feature table
Start End DB Term Name
17 153 Pfam PF00675 Insulinase (Peptidase family M16)
17 153 InterPro IPR011765 Peptidase M16, N-terminal
36 59 ProSitePatterns PS00143 Insulinase family, zinc-binding region signature.
36 59 InterPro IPR001431 Peptidase M16, zinc-binding site
591 756 SUPERFAMILY SSF63411 LuxS/MPP-like metallohydrolase
591 756 InterPro IPR011249 Metalloenzyme, LuxS/M16 peptidase-like
601 759 Gene3D G3DSA:3.30.830.10 -
5 211 SUPERFAMILY SSF63411 LuxS/MPP-like metallohydrolase
5 211 InterPro IPR011249 Metalloenzyme, LuxS/M16 peptidase-like
6 682 NCBIfam TIGR02110 pyrroloquinoline quinone biosynthesis protein PqqF
6 682 InterPro IPR011844 Coenzyme PQQ biosynthesis protein PqqF
2 225 Gene3D G3DSA:3.30.830.10 -
619 708 PANTHER PTHR43690 NARDILYSIN

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_A0A4S4WK18
AlphaFold full sequence Viewing
ColabFold VK055_0674
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 0.085
58 0.039
53 0.005
55 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 10.92 0.504
2 10.85 0.5
3 5.24 0.201
4 4.84 0.178
5 3.43 0.098

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.

99 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
1EF P14735 443.5 Da LogP 3.35 TPSA 109.1 ✓ Ro5 ✓ Clean Cc1ccc(cc1)C(=O)NCc2cn(nn2)[C@H](Cc3ccc4ccccc4c…
2PJ P14735 398.5 Da LogP 5.36 TPSA 51.2 1 viol. ✓ Clean CC(C)(C)OC(=O)NC[C@@H](Cc1cc2ccccc2nc1)c3cc(ccc…
2QW P14735 424.4 Da LogP 2.89 TPSA 84.2 ✓ Ro5 ✓ Clean Cc1ccc(cc1)NC(=O)[C@H](C2CCCCC2)NC(=O)[C@H](CC[…
2QX P14735 735.9 Da LogP 7.85 TPSA 126.6 2 viol. ✓ Clean COC(=O)NC[C@@H](Cc1cc2ccccc2nc1)c3cc(ccc3F)CCCC…
33K P14735 360.4 Da LogP 0.11 TPSA 135.6 ✓ Ro5 ✓ Clean c1ccc(cc1)CN(CC(=O)N[C@@H](Cc2cnc[nH]2)C(=O)O)C…
3M9 P14735 447.5 Da LogP 3.18 TPSA 109.1 ✓ Ro5 ✓ Clean c1ccc2cc(ccc2c1)C[C@H](CC(=O)NO)n3c(cnn3)CNC(=O…
6PE P31800 410.4 Da LogP 2.06 TPSA 137.2 ✓ Ro5 ✓ Clean CCCCCC(=O)OC[C@H](CO[P@](=O)([O-])OCCN)OC(=O)CC…
8PE P31800 692.0 Da LogP 10.50 TPSA 134.4 2 viol. ✓ Clean CCCCCCCCCCCCCCCCCC(=O)OC[C@H](CO[P@@](=O)(O)OCC…
9XE P31800 426.4 Da LogP 5.47 TPSA 64.2 1 viol. ✓ Clean CC1=C(Nc2cc(ccc2C1=O)OC)c3cc(cnc3)c4ccc(cc4)OC(…
AZO P31800 403.4 Da LogP 4.09 TPSA 103.6 ✓ Ro5 ✓ Clean COC=C(c1ccccc1Oc2cc(ncn2)Oc3ccccc3C#N)C(=O)OC
CDL P31800 1464.1 Da LogP 23.31 TPSA 242.6 3 viol. ✓ Clean CCCCCCCCCCCCCCCCCC(=O)OC[C@H](COP(=O)([O-])OCC(…
FES P31800 175.8 Da LogP 1.29 TPSA 0.0 ✓ Ro5 ✓ Clean S1[Fe]S[Fe]1
FNM P31800 311.4 Da LogP 3.49 TPSA 44.7 ✓ Ro5 ✓ Clean C[C@@]1(C(=O)N(C(=N1)SC)Nc2ccccc2)c3ccccc3
FX2 P31800 429.4 Da LogP 4.79 TPSA 65.7 ✓ Ro5 ✓ Clean CC1C(=O)c2ccc(cc2N=C1c3cnn(c3)Cc4ccc(cc4)OC(F)(…
J18 P14735 558.7 Da LogP 5.60 TPSA 60.9 2 viol. ✓ Clean Cc1cccc(c1C)c2ccc(cc2)[C@H]3[C@@H]4CN(CCCCN4[C@…
J22 P14735 494.7 Da LogP 3.32 TPSA 78.7 ✓ Ro5 ✓ Clean Cc1cccc(c1C)c2ccc(cc2)[C@H]3[C@@H]4CN(CCCCN4[C@…
JAG P31800 415.4 Da LogP 6.33 TPSA 47.9 1 viol. ✓ Clean CC1=NC2=C(CCCC2)C(=O)C1c3ccc(cc3)Oc4ccc(cc4)OC(…
JGW P31800 409.4 Da LogP 6.25 TPSA 38.7 1 viol. ✓ Clean CC1=Nc2ccccc2C(=O)C1c3ccc(cc3)Cc4ccc(cc4)OC(F)(…
JHB P31800 443.9 Da LogP 6.65 TPSA 42.1 1 viol. ✓ Clean CC1=C(Nc2cc(ccc2C1=O)Cl)c3ccc(cc3)Cc4ccc(cc4)OC…
JHE P31800 425.4 Da LogP 5.70 TPSA 51.5 1 viol. ✓ Clean CC1=C(N(c2ccccc2C1=O)O)c3ccc(cc3)Cc4ccc(cc4)OC(…
LMT P31800 510.6 Da LogP -0.45 TPSA 178.5 3 viol. ✓ Clean CCCCCCCCCCCCO[C@H]1[C@@H]([C@H]([C@@H]([C@H](O1…
MC3 P31800 677.9 Da LogP 9.05 TPSA 111.2 2 viol. ✓ Clean CCCCCCCCCCCCCC(=O)OC[C@H](CO[P@@](=O)([O-])OCC[…
MGH P14735 416.4 Da LogP 0.16 TPSA 141.7 ✓ Ro5 ✓ Clean COC(=O)[C@@H](Cc1c[nH]cn1)NC(=O)CN(CC(=O)O)C(=O…
MGJ P14735 401.5 Da LogP 0.20 TPSA 127.4 ✓ Ro5 ✓ Clean CNC(=O)[C@H](Cc1c[nH]cn1)NC(=O)C[N@](CCCc2ccccc…
MGK P14735 402.5 Da LogP 0.63 TPSA 124.6 ✓ Ro5 ✓ Clean COC(=O)[C@H](Cc1cnc[nH]1)NC(=O)C[N@](CCCc2ccccc…
MGW P14735 388.4 Da LogP 0.24 TPSA 124.6 ✓ Ro5 ✓ Clean COC(=O)[C@H](Cc1cnc[nH]1)NC(=O)C[N@@](CCc2ccccc…
MJM P31800 331.4 Da LogP 5.42 TPSA 38.7 1 viol. ✓ Clean CC1=C(C(=O)C2CCCCC2=N1)c3ccc(cc3)Oc4ccccc4
MYX P31800 487.7 Da LogP 5.82 TPSA 87.3 1 viol. ✓ Clean C[C@@H](/C=C/C=C/C(C)C)c1nc(cs1)c2nc(cs2)/C=C/[…
PEE P31800 744.0 Da LogP 11.61 TPSA 134.4 2 viol. ✓ Clean CCCCCCCC/C=C\CCCCCCCC(=O)OC[C@H](COP(=O)(O)OCCN…
PEF P31800 692.0 Da LogP 10.50 TPSA 134.4 2 viol. ✓ Clean CCCCCCCCCCCCCCCC(=O)OC[C@H](CO[P@@](=O)(O)OCCN)…
PLX P31800 767.1 Da LogP 11.61 TPSA 114.7 2 viol. ✓ Clean CCCCCCCCCCCCCCCCC[C@@H](O)O[C@H](CO[C@@H](CCCCC…
PX4 P31800 679.0 Da LogP 9.68 TPSA 108.4 2 viol. ✓ Clean CCCCCCCCCCCCCC(=O)OC[C@H](CO[P@](=O)(O)OCC[N+](…
PX6 P31800 647.9 Da LogP 9.88 TPSA 122.2 2 viol. ✓ Clean CCCCCCCCCCCCCCCC(=O)OC[C@H](CO[P@@](=O)(O)[O-])…
QIX P14735 542.6 Da LogP -1.64 TPSA 241.6 2 viol. ✓ Clean [H]/N=C(/N)\NCCC[C@@H](C(=O)NCC(=O)NCC(=O)N)NC(…

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.