Protein target profile

KP13_05028

NAD(P) transhydrogenase subunit beta

Genome: KpKP13 Gene: AHE44797.1 pntB 3D evidence: AlphaFold DB model + ColabFold model UniProt A0A0H3GSA5
Length 462
Pocket druggability 0.989
Direct ligand evidence 0 54 total records
Functional annotation 1 EC 4 GO
Target summary

Promising target candidate with multiple supporting evidence streams.

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 (%)
52.318 Lower values reduce human off-target concern.
Human E-value
9.01e-157
Gut microbiome similarity
5.3% of screened genomes Lower prevalence suggests narrower overlap with the screened gut microbiome.

Essentiality

Essential (DEG)
N
DEG identity (%)
0.0 Higher values support similarity to known essential genes.

Localization

Localization
CytoplasmicMembrane

Structure confidence

ColabFold pLDDT
91.03 0-100 confidence; >70 supports local structural interpretation.

Binding-site evidence

AlphaFold DB / UniProt model

The selected pocket score is the FPocket value used for ranking after applying the curated structure priority. It estimates small-molecule pocket quality; it is not experimental binding evidence. The 3D viewer may show a different loaded structure, so visible pockets can differ.

FPocket 0.989
Structure A0A0H3GSA5
Pocket Pocket 4
P2Rank 0.737
Structure A0A0H3GSA5
Pocket Pocket 1
ColabFold model
FPocket 0.984 · Pocket 1
P2Rank 0.693 · Pocket 1
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 253 / 4744 genomes with a hit
Prevalence 5.3%

Cross-references

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

Sequence

Primary amino-acid sequence viewer.

MSGGLVTAAYIVAAILFIFSLAGLSKHETSQQGNYFGIAGMAIALIATILGPDAGNVGWIILAMVIGGAIGIRLAKKVEMTEMPELVAILHSFVGLAAVLVGFNSYLQHETGMEQILVNIHLTEVFLGIFIGAVTFTGSVVAFGKLRGKISSRPLMLPNRHKLNLAALVVSFILMVIFVRSDSTGTQVLCLLVMTAIALAFGWHLVASIGGADMPVVVSMLNSYSGWAAAAAGFMLSNDLLIVTGALVGSSGAILSYIMCKAMNRSFISVIAGGFGTDGSSSGGDEEVGEHREISAEETAEMLKNSHSVIITPGYGMAVAQAQYPVAEITEKLRARGIKVRFGIHPVAGRLPGHMNVLLAEAKVPYDIVLEMDEINDDFSDTDTVLVIGANDTVNPAAQDDPKSPIAGMPVLEVWKAQNVVVFKRSMNTGYAGVQNPLFFKENTHMLFGDAKASVDAILKAL

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 4 GO

Enzyme Commission (EC)

1

Gene Ontology (GO)

4
  • GO:0050661 Binding to nicotinamide-adenine dinucleotide phosphate, a coenzyme involved in many redox and biosynthetic reactions; binding may be to either the oxidized form, NADP+, or the reduced form, NADPH.
  • GO:0016020 A lipid bilayer along with all the proteins and protein complexes embedded in it and attached to it.
  • GO:0008750 Catalysis of the reaction: H+(in) + NAD+ + NADPH = H+(out) + NADH + NADP+.
  • 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 domains and features

Domain and signature matches imported from InterPro and related databases.

37 records
Show feature table
Start End DB Term Name
1 462 PANTHER PTHR44758 NAD(P) TRANSHYDROGENASE SUBUNIT BETA
33 52 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
214 234 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
261 462 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
181 185 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
125 143 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
163 180 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
208 213 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
144 162 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
240 259 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
1 5 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
25 32 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
106 124 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
286 462 Gene3D G3DSA:3.40.50.1220 -
5 24 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
57 74 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
214 236 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
52 56 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
6 24 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
121 143 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
86 105 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
185 207 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
7 460 Pfam PF02233 NAD(P) transhydrogenase beta subunit
7 460 InterPro IPR034300 NADP transhydrogenase beta-like domain
33 51 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
75 85 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
87 106 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
289 462 SUPERFAMILY SSF52467 DHS-like NAD/FAD-binding domain
289 462 InterPro IPR029035 DHS-like NAD/FAD-binding domain superfamily
235 239 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
240 260 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
186 207 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
1 462 PIRSF PIRSF000204 PNTB
1 462 InterPro IPR012136 NADP transhydrogenase, beta subunit
57 74 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
163 180 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
285 462 FunFam G3DSA:3.40.50.1220:FF:000002 NAD(P) transhydrogenase subunit beta

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.

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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 · FPocket

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

Site 1 FPocket #4
0.989
Likely same site as P2Rank 2 5.5 Å 9 shared residues 50% of smaller site
Unusual size
Show in viewer
Surrounding area

Binding pockets · P2Rank

Probability: high ≥ 0.5 · medium 0.2–0.49 · low < 0.2

Site 1 P2Rank #1
0.737
Show in viewer
Surrounding area
Site 2 P2Rank #2
0.27
Likely same site as FPocket 4 5.5 Å 9 shared residues 50% of smaller site
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Surrounding area
Site 3 P2Rank #3
0.135
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Surrounding area
Site 4 P2Rank #4
0.079
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Surrounding area
Site 5 P2Rank #5
0.071
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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_A0A0H3GSA5
AlphaFold DB full sequence Viewing
ColabFold KP13_05028
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.

54 records
Chemistry signal

Structural ligand evidence is available for this target.

Direct evidence 0 same-protein records
Transferred evidence 4 records from similar proteins
Structural ligands 4 0 loaded crystals
Measured bioactivity 0 direct and transferred ChEMBL records
Proposed compounds 50 similarity-based ZINC candidates
Best available ligand signal
D12 PDB via homolog 170.3 Da · LogP 4.93 · TPSA 0.0 Open detail RCSB PDB
PC1 PDB via homolog Detail RCSB PDB
TXD PDB via homolog Detail RCSB PDB
TXP PDB via homolog Detail RCSB PDB
ZINC13544781 ZINC proposed compound · Tanimoto 0.780 Detail ZINC

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
D12 RCSB PDB W5PFI3 170.3 Da LogP 4.93 TPSA 0.0 ✓ Ro5 ✓ Clean CCCCCCCCCCCC
PC1 RCSB PDB W5PFI3 790.2 Da LogP 12.17 TPSA 111.2 2 viol. ✓ Clean CCCCCCCCCCCCCCCCCC(=O)OC[C@H](CO[P@@](=O)([O-])…
TXD RCSB PDB P0C188 667.5 Da LogP -3.30 TPSA 317.6 3 viol. ✓ Clean c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)…
TXP RCSB PDB P0C188 747.4 Da LogP -3.18 TPSA 364.1 3 viol. ✓ Clean c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)…

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.