KpKP13 Protein target profile

Soluble pyridine nucleotide transhydrogenase

Accession: KP13_00552

Gene: AHE47028.1 sthA 3D evidence: AlphaFold DB model + ColabFold model UniProt A0A0H3GLH6
Length 478
Pocket druggability (P2Rank · AlphaFold DB model) 0.964
Direct ligand evidence 0 66 total records
Functional annotation 1 EC 7 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 (%)
49.02 Lower values reduce human off-target concern.
Human E-value
5.83e-07
Gut microbiome similarity
2.9% of screened genomes Lower prevalence suggests narrower overlap with the screened gut microbiome.

Essentiality

Essential (DEG)
Y
DEG identity (%)
96.567 Higher values support similarity to known essential genes.
DEG E-value
0.0 Smaller values mean stronger essential-gene similarity.

Structure confidence

ColabFold pLDDT
93.06 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) 0.964
Structure A0A0H3GLH6
Pocket Pocket 1
Druggability (FPocket) 0.129
Structure A0A0H3GLH6
Pocket Pocket 11
ColabFold model
P2Rank 0.964 · Pocket 1
FPocket 0.17 · Pocket 20
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 137 / 4744 genomes with a hit
Prevalence 2.9%

Cross-references

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

Sequence

Primary amino-acid sequence viewer.

MFILCIKQVSNAMSHSWDYDAIVIGSGPGGEGAAMGLVKQGARVAVIERYHNVGGGCTHWGTIPSKALRHAVSRIIEFNQNPLYSDHSRLLRSSFADILNHADSVINQQTHMRQGFYERNHCEILQGNAHFVDEHTLALECHDGTVETVTAEKFVIACGSRPYHPADVDFHHPRIYDSDSILSLQHEPRHVIIYGAGVIGCEYASIFRGMEVKVDLINTRDRLLAFLDQEMSDSLSYHFWNSGVVIRHNEEYEKIEGVDDGVIMHLKSGKKLKADCLLYANGRTGNTDTLALENIGLQTDSRGQLKVNSMYQTALPHIYAVGDVIGYPSLASAAYDQGRIAAQALVKGEASAHLIEDIPTGIYTIPEISSVGKTEQQLTAMKVPYEVGRAQFKHLARAQIVGMSVGTLKILFHRETKEILGIHCFGERAAEIIHIGQAIMEQKGGGNTIEYFVNTTFNYPTMAEAYRVAALNGLNRLF

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 7 GO

Subcellular localization

Localization
Cytoplasmic

Enzyme Commission (EC)

1

Gene Ontology (GO)

7
  • GO:0003957 Catalysis of the reaction: NADPH + NAD+ = NADP+ + NADH.
  • GO:0016491 Catalysis of an oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced.
  • GO:0050660 Binding to FAD, flavin-adenine dinucleotide, the coenzyme or the prosthetic group of various flavoprotein oxidoreductase enzymes, in either the oxidized form, FAD, or the reduced form, FADH2.
  • GO:0005829 The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
  • GO:0004148 Catalysis of the reaction: N(6)-[(R)-dihydrolipoyl]-L-lysyl-[protein] + NAD+ = N(6)-[(R)-lipoyl]-L-lysyl-[protein] + NADH + H+.
  • GO:0006103 The chemical reactions and pathways involving oxoglutarate, the dianion of 2-oxoglutaric acid. It is a key constituent of the TCA cycle and a key intermediate in amino-acid metabolism.
  • GO:0006739 The chemical reactions and pathways involving nicotinamide adenine dinucleotide phosphate (NADP+), a coenzyme that interconverts with its reduced form, NADPH, in many redox and biosynthetic reactions.

Sequence domains and features

Domain and signature matches imported from InterPro and related databases.

35 records
Show feature table
Start End DB Term Name
19 345 Gene3D G3DSA:3.50.50.60 -
19 345 InterPro IPR036188 FAD/NAD(P)-binding domain superfamily
357 477 Gene3D G3DSA:3.30.390.30 -
357 477 InterPro IPR016156 FAD/NAD-linked reductase, dimerisation domain superfamily
14 478 Hamap MF_00247 Soluble pyridine nucleotide transhydrogenase [sthA].
14 478 InterPro IPR022962 Soluble pyridine nucleotide transhydrogenase, gammaproteobacteria
21 40 PRINTS PR00368 FAD-dependent pyridine nucleotide reductase signature
190 208 PRINTS PR00368 FAD-dependent pyridine nucleotide reductase signature
151 169 PRINTS PR00368 FAD-dependent pyridine nucleotide reductase signature
303 325 PRINTS PR00368 FAD-dependent pyridine nucleotide reductase signature
274 290 PRINTS PR00368 FAD-dependent pyridine nucleotide reductase signature
13 334 SUPERFAMILY SSF51905 FAD/NAD(P)-binding domain
13 334 InterPro IPR036188 FAD/NAD(P)-binding domain superfamily
16 472 PANTHER PTHR22912 DISULFIDE OXIDOREDUCTASE
170 288 Gene3D G3DSA:3.50.50.60 -
170 288 InterPro IPR036188 FAD/NAD(P)-binding domain superfamily
354 375 PRINTS PR00411 Pyridine nucleotide disulphide reductase class-I signature
20 42 PRINTS PR00411 Pyridine nucleotide disulphide reductase class-I signature
190 215 PRINTS PR00411 Pyridine nucleotide disulphide reductase class-I signature
444 464 PRINTS PR00411 Pyridine nucleotide disulphide reductase class-I signature
154 163 PRINTS PR00411 Pyridine nucleotide disulphide reductase class-I signature
275 289 PRINTS PR00411 Pyridine nucleotide disulphide reductase class-I signature
419 434 PRINTS PR00411 Pyridine nucleotide disulphide reductase class-I signature
318 325 PRINTS PR00411 Pyridine nucleotide disulphide reductase class-I signature
53 68 PRINTS PR00411 Pyridine nucleotide disulphide reductase class-I signature
170 288 FunFam G3DSA:3.50.50.60:FF:000008 Soluble pyridine nucleotide transhydrogenase
358 469 Pfam PF02852 Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain
358 469 InterPro IPR004099 Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain
357 475 SUPERFAMILY SSF55424 FAD/NAD-linked reductases, dimerisation (C-terminal) domain
357 475 InterPro IPR016156 FAD/NAD-linked reductase, dimerisation domain superfamily
4 475 PIRSF PIRSF000350 Hg-II_reductase_MerA
4 475 InterPro IPR001100 Pyridine nucleotide-disulphide oxidoreductase, class I
19 338 Pfam PF07992 Pyridine nucleotide-disulphide oxidoreductase
19 338 InterPro IPR023753 FAD/NAD(P)-binding domain
357 477 FunFam G3DSA:3.30.390.30:FF:000002 Soluble pyridine nucleotide transhydrogenase

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 · P2Rank

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

Pocket 1 P2Rank #1
0.964
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Surrounding area
Pocket 2 P2Rank #2
0.592
Show in viewer
Surrounding area
Pocket 3 P2Rank #3
0.292
Show in viewer
Surrounding area
Pocket 4 P2Rank #4
0.245
Show in viewer
Surrounding area
Pocket 5 P2Rank #5
0.052
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Surrounding area
Residue sets
UniProt: Binding site:14-23
UniProt: Binding site:161-168
UniProt: Binding site:248-248
UniProt: Binding site:289-289
UniProt: Binding site:32-32
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_A0A0H3GLH6
AlphaFold DB full sequence Viewing
ColabFold KP13_00552
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.

66 records
Chemistry signal

Structural and bioactivity evidence are both available for this target.

Direct evidence 0 same-protein records
Transferred evidence 16 records from similar proteins
Structural ligands 13 0 loaded crystals
Measured bioactivity 3 direct and transferred ChEMBL records
Proposed compounds 50 similarity-based ZINC candidates
Best available ligand signal
ACM PDB via homolog 59.1 Da · LogP -0.51 · TPSA 43.1 Open detail RCSB PDB
AUP PDB via homolog Detail RCSB PDB
BTB PDB via homolog Detail RCSB PDB
ELI PDB via homolog Detail RCSB PDB
GCG 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
ACM RCSB PDB P00390 59.1 Da LogP -0.51 TPSA 43.1 ✓ Ro5 ✓ Clean CC(=O)N
AUP RCSB PDB P00390 368.4 Da LogP 6.67 TPSA 25.8 1 viol. ✓ Clean c1ccc(cc1)p2c(c3c(c2c4ccccn4)CCCC3)c5ccccn5
BTB RCSB PDB P09622-2 209.2 Da LogP -3.01 TPSA 104.4 ✓ Ro5 ✓ Clean C(CO)N(CCO)C(CO)(CO)CO
ELI RCSB PDB P00390 286.3 Da LogP 3.42 TPSA 71.4 ✓ Ro5 Alert CC1=C(C(=O)c2ccccc2C1=O)CCCCCC(=O)O
GCG RCSB PDB P00390 723.9 Da LogP -4.58 TPSA 313.3 3 viol. ✓ Clean C(CCNC(=O)CNC(=O)[C@H](CS)NC(=O)CC[C@@H](C(=O)O…
GDS RCSB PDB P00390 612.6 Da LogP -3.88 TPSA 317.6 3 viol. ✓ Clean C(CC(=O)N[C@@H](CSSC[C@@H](C(=O)NCC(=O)O)NC(=O)…
GSH RCSB PDB P00390 307.3 Da LogP -2.21 TPSA 158.8 1 viol. ✓ Clean C(CC(=O)N[C@@H](CS)C(=O)NCC(=O)O)[C@@H](C(=O)O)N
HXP RCSB PDB P00390 286.3 Da LogP 3.20 TPSA 87.0 ✓ Ro5 ✓ Clean c1cc2c(cc1O)Oc3cc(ccc3C2CCC(=O)O)O
MLT RCSB PDB B4EEF2 134.1 Da LogP -1.09 TPSA 94.8 ✓ Ro5 ✓ Clean C([C@H](C(=O)O)O)C(=O)O
NHE RCSB PDB P09622-2 207.3 Da LogP 0.80 TPSA 66.4 ✓ Ro5 ✓ Clean C1CCC(CC1)NCCS(=O)(=O)O
RGS RCSB PDB P00390 612.6 Da LogP -3.88 TPSA 317.6 3 viol. ✓ Clean C(CNC(=O)[C@@H](CSSC[C@H](C(=O)NCC[C@@H](C(=O)O…
TS2 RCSB PDB P00390 721.9 Da LogP -4.04 TPSA 313.3 3 viol. ✓ Clean C1CCNC(=O)CNC(=O)[C@H](CSSC[C@@H](C(=O)NCC(=O)N…
TS4 RCSB PDB P00390 867.1 Da LogP -4.38 TPSA 377.3 3 viol. ✓ Clean C(CCNCCCNC(=O)CNC(=O)[C@H](CSSC[C@@H](C(=O)NCC(…

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.