Protein target profile

KP13_31580

Mercuric reductase

Genome: KpKP13 Gene: AHE47230.1 merA 3D evidence: AlphaFold DB model + ColabFold model UniProt A0A2D1HBC1
Length 564
Pocket druggability 0.997
Direct ligand evidence 0 72 total records
Functional annotation 1 EC 10 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 (%)
53.061 Lower values reduce human off-target concern.
Human E-value
2.46e-08
Gut microbiome similarity
0.4% 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
Cytoplasmic

Structure confidence

ColabFold pLDDT
93.16 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 0.997
Structure A0A2D1HBC1
Pocket Pocket 25
P2Rank 0.956
Structure A0A2D1HBC1
Pocket Pocket 1
ColabFold model
FPocket 0.853 · Pocket 26
P2Rank 0.957 · Pocket 1
Core conservation Accessory gene
Roary accessory
CoreCruncher accessory
Gut microbiome 21 / 4744 genomes with a hit
Prevalence 0.4%

Cross-references

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

Sequence

Primary amino-acid sequence viewer.

MSTLKITGMTCDSCAVHVKDALEKVPGVQSADVSYAKGSAKLAIEVGTSPDALTAAVAGLGYRATLADAPSVSTPGGLLDKMRDLLGRNDKTGSSGALHIAVIGSGGAAMAAALKAVEQGARVTLIERGTIGGTCVNVGCVPSKIMIRAAHIAHLRRESPFDGGIAATTPTIQRTALLAQQQARVDELRHAKYEGILEGNPAITVLHGSARFKDNRNLIVQLNDGGERVVAFDRCLIATGASPAVPPIPGLKDTPYWTSTEALVSETIPKRLAVIGSSVVALELAQAFARLGAKVTILARSTLFFREDPAIGEAVTAAFRMEGIEVREHTQASQVAYINGEGDGEFVLTTAHGELRADKLLVATGRAPNTRKLALDATGVTLTPQGAIVIDPGMRTSVEHIYAAGDCTDQPQFVYVAAAAGTRAAINMTGGDAALNLTAMPAVVFTDPQVATVGYSEAEAHHDGIKTDSRTLTLDNVPRALANFDTRGFIKLVVEEGSGRLIGVQAVAPEAGELIQTAALAIRNRMTVQELADQLFPYLTMVEGLKLAAQTFNKDVKQLSCCAG

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 10 GO

Enzyme Commission (EC)

1

Gene Ontology (GO)

10
  • GO:0045340 Binding to a mercury ion (Hg2+).
  • GO:0050787 Any process that reduce or remove the toxicity of mercuric ion. These include transport of mercury away from sensitive areas and to compartments or complexes whose purpose is sequestration of mercury ion and/or reduction of mercury ion (Hg[II]) to metallic mercury (Hg[0]).
  • GO:0016668 Catalysis of an oxidation-reduction (redox) reaction in which a sulfur-containing group acts as a hydrogen or electron donor and reduces NAD or NADP.
  • GO:0046872 Binding to a metal ion.
  • 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: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:0016152 Catalysis of the reaction: H+ + Hg + NADP+ = Hg2+ + NADPH.
  • GO:0003955 Catalysis of the reaction: NAD(P)H + H+ + a quinone = NAD(P)+ + a quinol.
  • GO:0006979 Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of oxidative stress, a state often resulting from exposure to high levels of reactive oxygen species, e.g. superoxide anions, hydrogen peroxide (H2O2), and hydroxyl radicals.

Sequence domains and features

Domain and signature matches imported from InterPro and related databases.

41 records
Show feature table
Start End DB Term Name
3 65 CDD cd00371 HMA
3 65 InterPro IPR006121 Heavy metal-associated domain, HMA
1 564 PIRSF PIRSF000350 Hg-II_reductase_MerA
1 564 InterPro IPR001100 Pyridine nucleotide-disulphide oxidoreductase, class I
1 69 Gene3D G3DSA:3.30.70.100 -
6 35 ProSitePatterns PS01047 Heavy-metal-associated domain.
6 35 InterPro IPR017969 Heavy-metal-associated, conserved site
96 558 PANTHER PTHR43014 MERCURIC REDUCTASE
100 460 SUPERFAMILY SSF51905 FAD/NAD(P)-binding domain
100 460 InterPro IPR036188 FAD/NAD(P)-binding domain superfamily
99 421 Pfam PF07992 Pyridine nucleotide-disulphide oxidoreductase
99 421 InterPro IPR023753 FAD/NAD(P)-binding domain
439 562 SUPERFAMILY SSF55424 FAD/NAD-linked reductases, dimerisation (C-terminal) domain
439 562 InterPro IPR016156 FAD/NAD-linked reductase, dimerisation domain superfamily
132 142 ProSitePatterns PS00076 Pyridine nucleotide-disulphide oxidoreductases class-I active site.
132 142 InterPro IPR012999 Pyridine nucleotide-disulphide oxidoreductase, class I, active site
2 70 SUPERFAMILY SSF55008 HMA, heavy metal-associated domain
2 70 InterPro IPR036163 Heavy metal-associated domain superfamily
439 564 Gene3D G3DSA:3.30.390.30 -
439 564 InterPro IPR016156 FAD/NAD-linked reductase, dimerisation domain superfamily
439 559 FunFam G3DSA:3.30.390.30:FF:000001 Dihydrolipoyl dehydrogenase
440 548 Pfam PF02852 Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain
440 548 InterPro IPR004099 Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain
99 564 NCBIfam TIGR02053 mercury(II) reductase
99 564 InterPro IPR021179 Mercury(II) reductase
1 65 ProSiteProfiles PS50846 Heavy-metal-associated domain profile.
1 65 InterPro IPR006121 Heavy metal-associated domain, HMA
244 364 Gene3D G3DSA:3.50.50.60 -
244 364 InterPro IPR036188 FAD/NAD(P)-binding domain superfamily
3 62 Pfam PF00403 Heavy-metal-associated domain
3 62 InterPro IPR006121 Heavy metal-associated domain, HMA
101 423 Gene3D G3DSA:3.50.50.60 -
101 423 InterPro IPR036188 FAD/NAD(P)-binding domain superfamily
236 253 PRINTS PR00945 Mercuric reductase class II signature
472 492 PRINTS PR00945 Mercuric reductase class II signature
271 288 PRINTS PR00945 Mercuric reductase class II signature
537 556 PRINTS PR00945 Mercuric reductase class II signature
109 127 PRINTS PR00945 Mercuric reductase class II signature
13 23 PRINTS PR00945 Mercuric reductase class II signature
144 163 PRINTS PR00945 Mercuric reductase class II signature
291 306 PRINTS PR00945 Mercuric reductase class II signature

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 #25
0.997
Likely same site as P2Rank 1 2.3 Å 37 shared residues 88% of smaller site
Unusual size
Show in viewer
Surrounding area
Site 2 FPocket #15
0.399
Likely same site as P2Rank 3 1.8 Å 10 shared residues 100% 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
0.956
Likely same site as FPocket 25 2.3 Å 37 shared residues 88% of smaller site
Show in viewer
Surrounding area
Site 2 P2Rank #2
0.334
Show in viewer
Surrounding area
Site 3 P2Rank #3
0.173
Likely same site as FPocket 15 1.8 Å 10 shared residues 100% of smaller site
Show in viewer
Surrounding area
Site 4 P2Rank #4
0.17
Show in viewer
Surrounding area
Site 5 P2Rank #5
0.051
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_A0A2D1HBC1
AlphaFold DB full sequence Viewing
ColabFold KP13_31580
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.

72 records
Chemistry signal

Structural and bioactivity evidence are both available for this target.

Direct evidence 0 same-protein records
Transferred evidence 22 records from similar proteins
Structural ligands 18 0 loaded crystals
Measured bioactivity 4 direct and transferred ChEMBL records
Proposed compounds 50 similarity-based ZINC candidates
Best available ligand signal
2JR PDB via homolog 351.5 Da · LogP 5.55 · TPSA 31.9 Open detail RCSB PDB
3II PDB via homolog Detail RCSB PDB
BTB PDB via homolog Detail RCSB PDB
GCG PDB via homolog Detail RCSB PDB
JWZ 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
2JR RCSB PDB Q389T8 351.5 Da LogP 5.55 TPSA 31.9 1 viol. ✓ Clean c1cc2c(cc[nH]2)cc1c3ncc(s3)C4(CCCCC4)N5CCCC5
3II RCSB PDB P9WHH9 625.6 Da LogP 4.65 TPSA 91.4 1 viol. ✓ Clean COc1ccc(c(c1)OC)C(=O)N2CCC3(CC2)C(=O)N(CN3c4ccc…
BTB RCSB PDB Q9A0E2 209.2 Da LogP -3.01 TPSA 104.4 ✓ Ro5 ✓ Clean C(CO)N(CCO)C(CO)(CO)CO
GCG RCSB PDB Q389T8 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…
JWZ RCSB PDB Q389T8 607.9 Da LogP 3.63 TPSA 103.4 1 viol. ✓ Clean [H]/N=C(/N)\N1CCC(CC1)(CN(C)CCCN2CN(C3(C2=O)CCN…
M52 RCSB PDB P9WHH9 429.3 Da LogP 1.69 TPSA 114.6 ✓ Ro5 ✓ Clean C[N@@](CC(=O)Nc1ccc(cc1)OC)S(=O)(=O)c2cc(cnc2N)…
M9J RCSB PDB Q389T8 555.8 Da LogP 6.51 TPSA 45.1 2 viol. ✓ Clean c1cc2c(ccn2CC3CCCN3)cc1c4nc(c(s4)C5(CCCCC5)N6CC…
M9S RCSB PDB Q389T8 434.7 Da LogP 5.77 TPSA 33.1 1 viol. ✓ Clean c1cc2c(ccn2C[C@@H]3CCCN3)cc1c4ncc(s4)C5(CCCCC5)…
M9Y RCSB PDB Q389T8 597.8 Da LogP 6.91 TPSA 45.1 2 viol. ✓ Clean c1cc2c(ccn2CCC3CCNCC3)cc1c4nc(c(s4)C5(CCCCC5)N6…
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
RBF RCSB PDB Q9A0E2 376.4 Da LogP -1.72 TPSA 161.6 ✓ Ro5 ✓ Clean Cc1cc2c(cc1C)N(C3=NC(=O)NC(=O)C3=N2)C[C@@H]([C@…
RD0 RCSB PDB Q389T8 462.7 Da LogP 6.41 TPSA 33.1 1 viol. ✓ Clean c1cc2c(ccn2CCC3CCNCC3)cc1c4ncc(s4)C5(CCCCC5)N6C…
RD7 RCSB PDB Q389T8 463.7 Da LogP 4.93 TPSA 36.3 ✓ Ro5 ✓ Clean c1cc2c(ccn2CCN3CCNCC3)cc1c4ncc(s4)C5(CCCCC5)N6C…
WP5 RCSB PDB Q389T8 373.2 Da LogP 4.08 TPSA 41.9 ✓ Ro5 ✓ Clean CC1=Nc2ccc(cc2[C@@H](N1CC(=O)OC)c3ccccc3)Br
WP6 RCSB PDB Q389T8 346.9 Da LogP 6.00 TPSA 15.6 1 viol. ✓ Clean CC1=Nc2ccc(cc2[C@@H](N1Cc3ccccc3)c4ccccc4)Cl
WP7 RCSB PDB Q389T8 463.0 Da LogP 4.85 TPSA 52.3 ✓ Ro5 ✓ Clean CC1=Nc2ccc(cc2[C@@H](N1CCN3CCN(CC3)C(=O)c4ccco4…
WPE RCSB PDB Q389T8 393.9 Da LogP 4.82 TPSA 57.8 ✓ Ro5 ✓ Clean CC1=Nc2ccc(cc2[C@@H](N1CCNC(=O)c3ccco3)c4ccccc4…
WPF RCSB PDB Q389T8 355.9 Da LogP 5.06 TPSA 18.8 1 viol. ✓ Clean Cc1ccc(cc1)[C@H]2c3cc(ccc3N=C(N2CCCN(C)C)C)Cl

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.