KpATCC43816 Protein target profile

nickel import ATP-binding protein NikE

Accession: VK055_0627

Gene: nikE AIK79250.1 3D evidence: AlphaFold DB model + ColabFold model Metabolism Not in network UniProt A0A0H3GNV2
Length 538
Pocket druggability (P2Rank · AlphaFold DB model) 0.878
Direct ligand evidence 0 55 total records
Functional annotation 0 EC 5 GO
Target summary

Target candidate with partial support; inspect missing evidence before prioritizing.

Automated synthesis of the evidence currently loaded. Review the underlying records before prioritizing this protein.

Terms and data sources used on this page

PDB: experimentally determined structures from the Protein Data Bank. These are the strongest structural evidence, but may cover only part of the protein.

AlphaFold DB model: a precomputed predicted structure downloaded from AlphaFold Database/UniProt, not an experiment performed here.

ColabFold model: a predicted structure generated for this workspace; interpret it with coverage and confidence.

pLDDT: confidence score for predicted structures. High values support local geometry; low values mean the region should not drive pocket interpretation.

FPocket / P2Rank: software tools that predict possible ligand-binding pockets on a 3D structure. They are useful screening signals, not experimental validation.

Druggability: a pocket-based estimate of whether a small molecule could bind productively. It does not mean a drug already exists.

PDB ligand: a compound observed in an experimental structure. Direct same-protein records are stronger than homolog-transferred records.

ChEMBL: a public database of measured compound bioactivity. Direct entries are stronger than entries transferred from similar proteins.

ZINC: a purchasable-compound database. Here it marks proposed candidates from chemical similarity, not measured binders.

LigQ / LigQ_2: an internal Target pipeline step that gathers PDB, ChEMBL, and ZINC ligand evidence for each protein.

Off-target: sequence similarity to proteins we prefer not to hit, such as human proteins or beneficial gut microbiome proteins.

DEG: Database of Essential Genes. A match suggests the protein resembles genes known to be essential in other organisms.

Roary / CoreCruncher: pan-genome tools used to decide whether a gene is core across analyzed strains or accessory/strain-specific.

EC / GO: functional annotations: EC describes enzyme reactions; GO describes biological process, molecular function, or cellular component.

KEGG pathway: a curated metabolic route label used here to group reactions imported from the metabolic model.

Chokepoint: a metabolic reaction that is the only producer or consumer of a metabolite in the imported model.

Prioritization evidence

Selectivity, essentiality, structural confidence, conservation, and predicted binding-site evidence.

Off-target risk

Human off-target
Hit
Human identity (%)
58.974 Lower values reduce human off-target concern.
Human E-value
2.24e-07
Gut microbiome similarity
0.9% of screened genomes Lower prevalence suggests narrower overlap with the screened gut microbiome.

Essentiality

Essential (DEG)
Y
DEG identity (%)
49.725 Higher values support similarity to known essential genes.
DEG E-value
6.9e-154 Smaller values mean stronger essential-gene similarity.

Structure confidence

ColabFold pLDDT
90.08 0-100 confidence; >70 supports local structural interpretation.

Binding-site evidence

AlphaFold DB / UniProt model

P2Rank's binding-site probability is the primary druggability signal shown across the app; FPocket's druggability score is shown alongside it for comparison. Both estimate small-molecule pocket quality after applying the curated structure priority — neither is experimental binding evidence. The 3D viewer may show a different loaded structure, so visible pockets can differ.

Druggability (P2Rank) 0.878
Structure A0A0H3GNV2
Pocket Pocket 1
Druggability (FPocket) 0.412
Structure A0A0H3GNV2
Pocket Pocket 29
ColabFold model
P2Rank 0.878 · Pocket 1
FPocket 0.441 · Pocket 12
Core conservation Accessory gene
Roary core
CoreCruncher accessory
Gut microbiome 43 / 4744 genomes with a hit
Prevalence 0.9%

Metabolic context

Reactions catalyzed, pathway membership, and centrality in the genome-scale metabolic network.

This protein is not associated with the imported metabolic network for this genome.

Browse the genome's metabolic network

Imported from KpATCC43816.sbml · 2026-07-09

Sequence

Primary amino-acid sequence viewer.

MTVLSVEDLRISYRSRGEWREVVHNISFSIQRGEMLAFVGESGSGKTTTAQAIIGLLADNARRDAGRIVLNGEVISDWSDKRLNRLRGVSISLVPQDPGNSLNPVKTIGQQVEEILRLHQSLSAAERRQQVLNLLAKVGLSHPEQRFDQYPHQLSGGMKQRVLIAIAIALQPDLIIADEPTSALDVTVQKRILDLLDILRRESGTAVLFVTHDLALAAERADRIMVFRQGEIQEQGATETIVQRPQHPYTRQLLHDLQDAPLRLTAARHRPLATPAIRVEGISKRFSLGKQALQALDSVSFEVRRGSTHALVGESGSGKTTLARILLGFERADAGQVIIDGIDAGHLSREAQRQLRRKIQFVYQNPFASLDPRQTLFAIIEEPLKNFERLSAATRRQRVESVAARVALAPELLSRTPRELSGGQRQRVAIARALILEPAILVLDEATSALDVTVQAQILALLQQLQQQLGLSYLFITHDLATVRRIADSVTVLRAGQVVEHGDVNRLFAAPQQAYTRELIAAIPQVSSRLAQAHTENA

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

5 GO

Subcellular localization

Localization
CytoplasmicMembrane

Gene Ontology (GO)

5
  • GO:0005524 Binding to ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
  • GO:0015833 The directed movement of peptides, compounds of two or more amino acids where the alpha carboxyl group of one is bound to the alpha amino group of another, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
  • GO:0000166 Binding to a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
  • GO:0016887 Catalysis of the reaction: ATP + H2O = ADP + H+ phosphate. ATP hydrolysis is used in some reactions as an energy source, for example to catalyze a reaction or drive transport against a concentration gradient.
  • GO:0055085 The process in which a solute is transported across a lipid bilayer, from one side of a membrane to the other.

Sequence domains and features

Domain and signature matches imported from InterPro and related databases.

32 records
Show feature table
Start End DB Term Name
276 538 Gene3D G3DSA:3.40.50.300 -
276 538 InterPro IPR027417 P-loop containing nucleoside triphosphate hydrolase
1 275 Gene3D G3DSA:3.40.50.300 -
1 275 InterPro IPR027417 P-loop containing nucleoside triphosphate hydrolase
4 254 ProSiteProfiles PS50893 ATP-binding cassette, ABC transporter-type domain profile.
4 254 InterPro IPR003439 ABC transporter-like, ATP-binding domain
420 434 ProSitePatterns PS00211 ABC transporters family signature.
420 434 InterPro IPR017871 ABC transporter-like, conserved site
277 502 CDD cd03257 ABC_NikE_OppD_transporters
277 519 SUPERFAMILY SSF52540 P-loop containing nucleoside triphosphate hydrolases
277 519 InterPro IPR027417 P-loop containing nucleoside triphosphate hydrolase
3 253 SUPERFAMILY SSF52540 P-loop containing nucleoside triphosphate hydrolases
3 253 InterPro IPR027417 P-loop containing nucleoside triphosphate hydrolase
3 236 CDD cd03257 ABC_NikE_OppD_transporters
499 530 Pfam PF08352 Oligopeptide/dipeptide transporter, C-terminal region
499 530 InterPro IPR013563 Oligopeptide/dipeptide ABC transporter, C-terminal
234 255 Pfam PF08352 Oligopeptide/dipeptide transporter, C-terminal region
234 255 InterPro IPR013563 Oligopeptide/dipeptide ABC transporter, C-terminal
296 448 Pfam PF00005 ABC transporter
296 448 InterPro IPR003439 ABC transporter-like, ATP-binding domain
277 520 ProSiteProfiles PS50893 ATP-binding cassette, ABC transporter-type domain profile.
277 520 InterPro IPR003439 ABC transporter-like, ATP-binding domain
1 270 FunFam G3DSA:3.40.50.300:FF:000016 Oligopeptide ABC transporter ATP-binding component
305 505 SMART SM00382 AAA_5
305 505 InterPro IPR003593 AAA+ ATPase domain
32 231 SMART SM00382 AAA_5
32 231 InterPro IPR003593 AAA+ ATPase domain
24 182 Pfam PF00005 ABC transporter
24 182 InterPro IPR003439 ABC transporter-like, ATP-binding domain
274 532 PANTHER PTHR43776 TRANSPORT ATP-BINDING PROTEIN
154 168 ProSitePatterns PS00211 ABC transporters family signature.
154 168 InterPro IPR017871 ABC transporter-like, conserved site

3D structure

Selected loaded structure. Experimental PDB entries may cover only a portion of the sequence; AlphaFold DB and ColabFold models typically cover the full protein but remain computational predictions.

Download VMD script Full viewer

Loading 3D structure...

Drag to rotate — click the view, then scroll to zoom.

Pocket score High Medium Low
How colors and pocket overlays are used
Uniform protein color marks the displayed model as a single molecular object.
Experimental PDB structures may be colored by chain to distinguish subunits or copies present in the file.
Pocket colors and alpha spheres are evidence overlays for predicted binding cavities; they are not alternative protein chains.
'Alpha spheres' is FPocket's own cavity-shape geometry, imported when available and aligned with the loaded structure.
'Pocket atoms'/'Predicted site atoms' show the pocket's residue atoms instead: P2Rank reports residues rather than alpha spheres, and FPocket falls back to this when alpha-sphere geometry is unavailable or doesn't align.
'No pocket geometry' means neither alpha spheres nor residue-position data could be found for that pocket; the layer just highlights the same residues as 'Nearby residues'.
Pocket details Inspect a specific pocket, or open the full viewer

Binding pockets · P2Rank

Druggability (P2Rank): high ≥ 0.5 · medium 0.2–0.49 · low < 0.2

Pocket 1 P2Rank #1
0.878
Likely same site as FPocket 1 4.0 Å 25 shared residues 100% of smaller site
Show in viewer
Surrounding area
Pocket 2 P2Rank #2
0.292
Show in viewer
Surrounding area
Pocket 3 P2Rank #3
0.233
Show in viewer
Surrounding area
Pocket 4 P2Rank #4
0.22
Likely same site as FPocket 29 4.2 Å 13 shared residues 72% of smaller site
Show in viewer
Surrounding area
Pocket 5 P2Rank #5
0.205
Show in viewer
Surrounding area

Binding pockets · FPocket

Druggability (FPocket): high ≥ 0.7 · medium 0.4–0.69 · low < 0.4

Pocket 1 FPocket #29
0.412
Likely same site as P2Rank 4 4.2 Å 13 shared residues 72% of smaller site
Show in viewer
Surrounding area
Pocket 2 FPocket #4
0.372
Show in viewer
Surrounding area
Pocket 3 FPocket #1
0.302 Unusual size
Likely same site as P2Rank 1 4.0 Å 25 shared residues 100% of smaller site
Show in viewer
Surrounding area
Pocket 4 FPocket #18
0.285 Unusual size
Show in viewer
Surrounding area
All structural evidence 0 experimental · 2 predicted

Structural evidence

0 + 2

Experimental PDB entries plus predicted AlphaFold DB or ColabFold models. Click Switch to display a different loaded structure in the viewer.

Entry Method Resolution Chain Coverage Links Status
AlphaFold DB AF_A0A0H3GNV2
AlphaFold DB full sequence Viewing
ColabFold VK055_0627
ColabFold full sequence Loaded

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.

55 records
Chemistry signal

Structural ligand evidence is available for this target.

Direct evidence 0 same-protein records
Transferred evidence 5 records from similar proteins
Structural ligands 5 0 loaded crystals
Measured bioactivity 0 direct and transferred ChEMBL records
Proposed compounds 50 similarity-based ZINC candidates
Best available ligand signal
AGS PDB via homolog 523.2 Da · LogP -1.51 · TPSA 262.1 Open detail RCSB PDB
ANP PDB via homolog Detail RCSB PDB
AT4 PDB via homolog Detail RCSB PDB
DMU PDB via homolog Detail RCSB PDB
POP PDB via homolog Detail RCSB PDB

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
AGS RCSB PDB D0VWX4 523.2 Da LogP -1.51 TPSA 262.1 3 viol. ✓ Clean c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)…
ANP RCSB PDB D0VWX4 506.2 Da LogP -2.06 TPSA 281.9 3 viol. ✓ Clean c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)…
AT4 RCSB PDB D0VWX4 443.3 Da LogP -0.81 TPSA 212.4 2 viol. ✓ Clean c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)…
DMU RCSB PDB A0A100XE85 482.6 Da LogP -1.23 TPSA 178.5 2 viol. ✓ Clean CCCCCCCCCCO[C@H]1[C@@H]([C@H]([C@@H]([C@H](O1)C…
POP RCSB PDB O57933 176.0 Da LogP -2.08 TPSA 129.9 ✓ Ro5 ✓ Clean O[P@@](=O)([O-])O[P@@](=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.

Cross-references

External database identifiers for this protein, its structures, ligands, and metabolic reactions.