Protein profile

VK055_4455

NADH dehydrogenase family protein

Genome: KpATCC43816

Gene: AIK82998.1 Structure source: AlphaFold + ColabFold UniProt A0A0H3GS64
Amino acids 307
Annotations 2
Features 35
PDB binders 23
Druggability 0.998

Overview

Basic information about this protein and its source genome.

Accession
VK055_4455
Gene
AIK82998.1
Status
annotated
Amino acids
307
Structure source
AlphaFold + ColabFold

Target profile

Computed evidence for target prioritization.

Human off-target
No hit
Human identity (%)
0.0
Gut microbiome off-target
hit
Essential (DEG)
N
DEG identity (%)
30.846
Localization
CytoplasmicMembrane
ColabFold pLDDT
95.08

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 0.998
Structure A0A0H3GS64
Pocket Pocket 1
P2Rank 0.713
Structure A0A0H3GS64
Pocket Pocket 1
ColabFold model
FPocket 0.97 · Pocket 2
P2Rank 0.655 · Pocket 1
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 107 / 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.

2 GO

Gene Ontology (GO)

2
  • GO:0016020 A lipid bilayer along with all the proteins and protein complexes embedded in it and attached to it.
  • GO:0005886 The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.

Sequence Features

Domain/signature hits from InterPro and related databases.

35 records
Show feature table
Start End DB Term Name
241 251 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
153 163 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
289 306 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
1 22 Phobius SIGNAL_PEPTIDE Signal peptide region
87 92 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
5 27 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
252 274 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
61 83 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
66 86 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
287 306 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
112 130 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
307 307 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
169 188 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
15 22 Phobius SIGNAL_PEPTIDE_C_REGION C-terminal region of a signal peptide.
38 53 ProSitePatterns PS00667 Respiratory-chain NADH dehydrogenase subunit 1 signature 1.
38 53 InterPro IPR018086 NADH:ubiquinone oxidoreductase, subunit 1, conserved site
1 22 SignalP_EUK SignalP-TM SignalP-TM
3 14 Phobius SIGNAL_PEPTIDE_H_REGION Hydrophobic region of a signal peptide.
189 218 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
93 111 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
132 154 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
275 288 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
131 152 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
1 2 Phobius SIGNAL_PEPTIDE_N_REGION N-terminal region of a signal peptide.
2 306 PANTHER PTHR43359 FORMATE HYDROGENLYASE SUBUNIT 4
219 240 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
164 188 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
252 274 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
7 301 Pfam PF00146 NADH dehydrogenase
7 301 InterPro IPR001694 NADH:ubiquinone oxidoreductase, subunit 1/F420H2 oxidoreductase subunit H
93 112 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
229 248 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
23 65 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
194 207 ProSitePatterns PS00668 Respiratory-chain NADH dehydrogenase subunit 1 signature 2.
194 207 InterPro IPR018086 NADH:ubiquinone oxidoreductase, subunit 1, conserved site

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_A0A0H3GS64
AlphaFold full sequence Viewing
ColabFold VK055_4455
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 0.998
21 0.701

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 11.76 0.624
2 10.67 0.573
3 5.88 0.288
4 2.32 0.059
5 1.5 0.021

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.

102 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
3PE O78747 748.1 Da LogP 12.06 TPSA 134.4 2 viol. ✓ Clean CCCCCCCCCCCCCCCCCC(=O)OC[C@H](COP(=O)(O)OCCN)OC…
970 O78747 394.4 Da LogP 3.70 TPSA 63.2 ✓ Ro5 ✓ Clean CC(=C)[C@H]1Cc2c(ccc3c2O[C@@H]4COc5cc(c(cc5[C@@…
AYA O78747 131.1 Da LogP -0.40 TPSA 66.4 ✓ Ro5 ✓ Clean C[C@@H](C(=O)O)NC(=O)C
CDL Q9B6E8 1464.1 Da LogP 23.31 TPSA 242.6 3 viol. ✓ Clean CCCCCCCCCCCCCCCCCC(=O)OC[C@H](COP(=O)([O-])OCC(…
CPL Q9B6E8 758.1 Da LogP 10.94 TPSA 111.2 2 viol. ✓ Clean CCCCCCCCCCCCCCCC(=O)OC[C@H](CO[P@@](=O)([O-])OC…
DCQ O78747 322.4 Da LogP 4.49 TPSA 52.6 ✓ Ro5 Alert CCCCCCCCCCC1=C(C(=O)C(=C(C1=O)OC)OC)C
EHZ Q9B6E8 584.7 Da LogP 3.04 TPSA 182.5 2 viol. ✓ Clean CCCCCCCCCCC[C@@H](CC(=O)SCCNC(=O)CCNC(=O)[C@@H]…
FES P03887 175.8 Da LogP 1.29 TPSA 0.0 ✓ Ro5 ✓ Clean S1[Fe]S[Fe]1
FME O78747 177.2 Da LogP -0.06 TPSA 66.4 ✓ Ro5 ✓ Clean CSCC[C@@H](C(=O)O)NC=O
HQK Q60019 364.9 Da LogP 5.24 TPSA 34.9 1 viol. ✓ Clean CC(C)(C)c1ccc(cc1)CSC2=C(C(=O)N(N=C2)C(C)(C)C)Cl
LMN Q9B6E8 1005.2 Da LogP -1.68 TPSA 357.1 3 viol. ✓ Clean CCCCCCCCCCC(CCCCCCCCCC)(CO[C@@H]1[C@@H]([C@@H](…
LMT Q9B6E8 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…
MYR O78747 228.4 Da LogP 4.77 TPSA 37.3 ✓ Ro5 ✓ Clean CCCCCCCCCCCCCC(=O)O
PC1 P03887 790.2 Da LogP 12.17 TPSA 111.2 2 viol. ✓ Clean CCCCCCCCCCCCCCCCCC(=O)OC[C@H](CO[P@@](=O)([O-])…
PEE O79874 744.0 Da LogP 11.61 TPSA 134.4 2 viol. ✓ Clean CCCCCCCC/C=C\CCCCCCCC(=O)OC[C@H](COP(=O)(O)OCCN…
PLC Q9B6E8 622.8 Da LogP 8.12 TPSA 108.4 2 viol. ✓ Clean CCCCCCCCCCCC(=O)OC[C@H](CO[P@](=O)(O)OCC[N+](C)…
PLX O79874 767.1 Da LogP 11.61 TPSA 114.7 2 viol. ✓ Clean CCCCCCCCCCCCCCCCC[C@@H](O)O[C@H](CO[C@@H](CCCCC…
PNS O78747 358.4 Da LogP -0.96 TPSA 145.2 1 viol. ✓ Clean CC(C)(COP(=O)(O)O)[C@H](C(=O)NCCC(=O)NCCS)O
PSC Q9B6E8 759.1 Da LogP 11.58 TPSA 108.4 2 viol. ✓ Clean CCCCCCCCCCCCCCCC(=O)OC[C@H](CO[P@@](=O)(O)OCC[N…
T7X Q9B6E8 887.1 Da LogP 9.17 TPSA 209.5 4 viol. ✓ Clean CCCCCCCCCCCCCCCCCC(=O)OC[C@H](COP(=O)(O)OC1[C@@…
UQ2 P03887 318.4 Da LogP 4.04 TPSA 52.6 ✓ Ro5 Alert CC1=C(C(=O)C(=C(C1=O)OC)OC)C\C=C(/C)\CCC=C(C)C
UQ9 Q9B6E8 795.2 Da LogP 16.13 TPSA 52.6 2 viol. Alert CC1=C(C(=O)C(=C(C1=O)OC)OC)C\C=C(/C)\CC\C=C(/C)…
ZMP O78747 568.7 Da LogP 4.07 TPSA 162.3 1 viol. ✓ Clean CCCCCCCCCCCCCC(=O)SCCNC(=O)CCNC(=O)[C@H](C(C)(C…

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.