KpKP13 Protein target profile

ADP compounds hydrolase nudE

Accession: KP13_09841

Gene: ANJ86570.1 nudE 3D evidence: AlphaFold DB model + ColabFold model UniProt A0A0H3GYF3
Length 186
Pocket druggability (P2Rank · AlphaFold DB model) 0.035
Direct ligand evidence 0 109 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 (%)
29.907 Lower values reduce human off-target concern.
Human E-value
9.5e-09
Gut microbiome similarity
3.3% 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.

Structure confidence

ColabFold pLDDT
97.0 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) 0.035
Structure A0A0H3GYF3
Pocket Pocket 1
Druggability (FPocket) 0.306
Structure A0A0H3GYF3
Pocket Pocket 10
ColabFold model
P2Rank 0.058 · Pocket 1
FPocket 0.272 · Pocket 14
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 157 / 4744 genomes with a hit
Prevalence 3.3%

Cross-references

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

Sequence

Primary amino-acid sequence viewer.

MSKSLQKPTILNVETVARSRLFNVESVDLEFSNGVRRVYERMRPSTREAVMIVPIVDDHIILIREYAVGTESYELGFSKGLIDPGETVDEAANRELKEEVGYGANKLTFLKKLSMAPSYFSSKMNIMVAEDLYPETLPGDEPEPLPQVRWPLAQLMSLLDEEDFNEARNVSALFLVREWLQAQGRL

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

5 GO

Subcellular localization

Localization
Cytoplasmic

Gene Ontology (GO)

5
  • GO:0016787 Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc.
  • GO:0005829 The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
  • GO:0019144 Catalysis of the reaction: ADP-sugar + H2O = AMP + alpha-D-aldose 1-phosphate.
  • GO:0006753 The chemical reactions and pathways involving any phosphorylated nucleoside.
  • GO:0019693 The chemical reactions and pathways involving ribose phosphate, any phosphorylated ribose sugar.

Sequence domains and features

Domain and signature matches imported from InterPro and related databases.

12 records
Show feature table
Start End DB Term Name
47 159 Pfam PF00293 NUDIX domain
47 159 InterPro IPR000086 NUDIX hydrolase domain
29 175 PANTHER PTHR11839 UDP/ADP-SUGAR PYROPHOSPHATASE
80 101 ProSitePatterns PS00893 Nudix box signature.
80 101 InterPro IPR020084 NUDIX hydrolase, conserved site
8 185 Gene3D G3DSA:3.90.79.10 Nucleoside Triphosphate Pyrophosphohydrolase
3 181 SUPERFAMILY SSF55811 Nudix
3 181 InterPro IPR015797 NUDIX hydrolase-like domain superfamily
8 185 FunFam G3DSA:3.90.79.10:FF:000006 ADP compounds hydrolase NudE
45 172 ProSiteProfiles PS51462 Nudix hydrolase domain profile.
45 172 InterPro IPR000086 NUDIX hydrolase domain
49 179 CDD cd03424 ADPRase_NUDT5

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

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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
0.035
Show in viewer
Surrounding area
Pocket 2 P2Rank #2
0.01
Show in viewer
Surrounding area
Pocket 3 P2Rank #3
0.006
Show in viewer
Surrounding area

Binding pockets · FPocket

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

Pocket 1 FPocket #10
0.306
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_A0A0H3GYF3
AlphaFold DB full sequence Viewing
ColabFold KP13_09841
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.

109 records
Chemistry signal

Structural and bioactivity evidence are both available for this target.

Direct evidence 0 same-protein records
Transferred evidence 59 records from similar proteins
Structural ligands 54 0 loaded crystals
Measured bioactivity 5 direct and transferred ChEMBL records
Proposed compounds 50 similarity-based ZINC candidates
Best available ligand signal
6SU PDB via homolog 229.3 Da · LogP 0.84 · TPSA 72.5 Open detail RCSB PDB
8DD PDB via homolog Detail RCSB PDB
8GD PDB via homolog Detail RCSB PDB
8OG PDB via homolog Detail RCSB PDB
958 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
6SU RCSB PDB Q9UKK9 229.3 Da LogP 0.84 TPSA 72.5 ✓ Ro5 ✓ Clean COC(=O)c1cccc(c1)NS(=O)(=O)C
8DD RCSB PDB Q9UKK9 427.2 Da LogP -1.42 TPSA 232.3 2 viol. ✓ Clean c1nc(c2c(n1)N(C(=O)N2)[C@H]3C[C@@H]([C@H](O3)CO…
8GD RCSB PDB Q9UKK9 443.2 Da LogP -2.13 TPSA 252.3 2 viol. ✓ Clean C1[C@@H]([C@H](O[C@H]1N2C3=C(C(=O)NC(=N3)N)NC2=…
8OG RCSB PDB Q9UKK9 363.2 Da LogP -2.25 TPSA 205.8 1 viol. ✓ Clean C1[C@@H]([C@H](O[C@H]1N2C3=C(C(=O)NC(=N3)N)NC2=…
958 RCSB PDB Q9UKK9 395.4 Da LogP 0.91 TPSA 104.0 ✓ Ro5 ✓ Clean Cc1cccc(c1)c2nnc(o2)Cn3c4c(nc3N(C)C)N(C(=O)N(C4…
ADV RCSB PDB Q9UKK9 557.3 Da LogP -3.17 TPSA 282.3 3 viol. ✓ Clean c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)…
APR RCSB PDB P45799 559.3 Da LogP -3.28 TPSA 291.5 3 viol. ✓ Clean c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)…
AR6 RCSB PDB Q5SKW5 559.3 Da LogP -3.28 TPSA 291.5 3 viol. ✓ Clean c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)…
ELQ RCSB PDB Q9UKK9 240.3 Da LogP 1.35 TPSA 23.6 ✓ Ro5 ✓ Clean CN1CCN(CC1)C(=O)c2ccc(c(c2)F)F
GQJ RCSB PDB Q9UKK9 239.2 Da LogP 0.03 TPSA 80.0 ✓ Ro5 ✓ Clean COC(=O)[C@@H]1C[C@H](CN1C(=O)c2ccco2)O
JH4 RCSB PDB Q9UKK9 109.1 Da LogP 0.52 TPSA 37.8 ✓ Ro5 ✓ Clean CNc1ncccn1
JJM RCSB PDB Q9UKK9 239.3 Da LogP 2.42 TPSA 55.6 ✓ Ro5 ✓ Clean Cc1cccc(c1)Nc2c3cnn(c3ncn2)C
JMM RCSB PDB Q9UKK9 248.3 Da LogP 0.97 TPSA 53.8 ✓ Ro5 ✓ Clean c1cc(oc1)C(=O)N2CCN(CC2)C(=O)C3CC3
K04 RCSB PDB Q9UKK9 213.3 Da LogP 0.90 TPSA 64.1 ✓ Ro5 ✓ Clean C[C@H]1CCO[C@@H]1C(=O)Nc2cnns2
K07 RCSB PDB Q9UKK9 227.7 Da LogP 1.60 TPSA 38.2 ✓ Ro5 ✓ Clean CN(C[C@H]1CCOC1)c2c(cncn2)Cl
K0A RCSB PDB Q9UKK9 210.3 Da LogP 2.00 TPSA 33.2 ✓ Ro5 ✓ Clean Cc1c(nc(s1)C)C(=O)N2CCCC2
K0D RCSB PDB Q9UKK9 227.3 Da LogP 0.79 TPSA 55.3 ✓ Ro5 ✓ Clean C[C@@H]1CN([C@H](CO1)C)C(=O)c2cnsn2
K0G RCSB PDB Q9UKK9 213.2 Da LogP 2.73 TPSA 54.0 ✓ Ro5 ✓ Clean c1ccc(cc1)NC(=O)Nc2cccnc2
K0J RCSB PDB Q9UKK9 140.1 Da LogP -0.45 TPSA 70.7 ✓ Ro5 ✓ Clean CCNC(=O)c1c[nH]nn1
K0M RCSB PDB Q9UKK9 206.2 Da LogP 0.97 TPSA 73.0 ✓ Ro5 ✓ Clean Cc1cc(on1)C(=O)Nc2ccn(n2)C
K0P RCSB PDB Q9UKK9 230.3 Da LogP 1.23 TPSA 59.8 ✓ Ro5 ✓ Clean CCn1cc(cn1)CNC(=O)c2cccnc2
K0S RCSB PDB Q9UKK9 248.3 Da LogP 2.14 TPSA 67.8 ✓ Ro5 ✓ Clean CCCc1nnc(s1)NC(=O)c2ccccn2
K0V RCSB PDB Q9UKK9 242.3 Da LogP 1.38 TPSA 58.6 ✓ Ro5 ✓ Clean CC(C)(C)NC(=O)N1CCC(CC1)C(=O)OC
K0Y RCSB PDB Q9UKK9 198.2 Da LogP -0.11 TPSA 81.4 ✓ Ro5 ✓ Clean Cc1cc(no1)C(=O)NCC(=O)OC
K1A RCSB PDB Q9UKK9 225.3 Da LogP 1.27 TPSA 60.9 ✓ Ro5 ✓ Clean Cc1c(c(on1)C)CN2C(=O)SC(=N2)C
K1D RCSB PDB Q9UKK9 175.2 Da LogP 0.56 TPSA 57.7 ✓ Ro5 ✓ Clean c1[nH]c2c(n1)c(ncn2)N3CCC3
K1G RCSB PDB Q9UKK9 205.3 Da LogP 1.21 TPSA 46.8 ✓ Ro5 ✓ Clean CC(C)N(C)c1c2cnn(c2ncn1)C
K1S RCSB PDB Q9UKK9 205.3 Da LogP 1.28 TPSA 46.3 ✓ Ro5 ✓ Clean CCN(CC)c1cc(nc2n1ncn2)C
K1V RCSB PDB Q9UKK9 170.2 Da LogP -0.27 TPSA 63.4 ✓ Ro5 ✓ Clean CC(=O)N1CCC[C@H](C1)C(=O)N
K1Y RCSB PDB Q9UKK9 248.3 Da LogP 3.30 TPSA 51.2 ✓ Ro5 ✓ Clean Cc1nc(c(s1)NC(=O)OC)c2ccccc2
K24 RCSB PDB Q9UKK9 156.2 Da LogP 0.81 TPSA 42.0 ✓ Ro5 ✓ Clean Cc1ncc(s1)C(=O)NC
K2J RCSB PDB Q9UKK9 139.2 Da LogP 0.53 TPSA 47.0 ✓ Ro5 ✓ Clean CNc1nccc(n1)OC
K2M RCSB PDB Q9UKK9 223.2 Da LogP 0.12 TPSA 79.8 ✓ Ro5 ✓ Clean c1cc(oc1)C(=O)N2CCN(CC2)C(=O)N
K2P RCSB PDB Q9UKK9 206.1 Da LogP 2.28 TPSA 46.5 ✓ Ro5 ✓ Clean c1ccc(c(c1)C(=O)O)OC(F)(F)F
K2S RCSB PDB Q9UKK9 203.3 Da LogP 0.28 TPSA 66.1 ✓ Ro5 ✓ Clean Cc1c(c(n[nH]1)C)S(=O)(=O)N(C)C
K2V RCSB PDB Q9UKK9 199.3 Da LogP 2.16 TPSA 51.8 ✓ Ro5 ✓ Clean C[C@H](c1ccc(cc1)c2cncnc2)N
K31 RCSB PDB Q9UKK9 187.2 Da LogP 2.28 TPSA 54.7 ✓ Ro5 ✓ Clean Cc1c(c(n[nH]1)C)c2ccccc2N
K34 RCSB PDB Q9UKK9 152.2 Da LogP 0.93 TPSA 54.5 ✓ Ro5 ✓ Clean c1csc(n1)c2[nH]ncn2
K3A RCSB PDB Q9UKK9 139.2 Da LogP 0.68 TPSA 57.8 ✓ Ro5 ✓ Clean Cc1cc(n[nH]1)NC(=O)C
K3D RCSB PDB Q9UKK9 199.3 Da LogP -0.12 TPSA 52.7 ✓ Ro5 ✓ Clean CCNC(=O)N1CCN(CC1)C(=O)C
K3J RCSB PDB Q9UKK9 137.2 Da LogP 1.22 TPSA 37.8 ✓ Ro5 ✓ Clean CCNc1ccc(nn1)C
K3P RCSB PDB Q9UKK9 210.6 Da LogP 1.66 TPSA 52.8 ✓ Ro5 ✓ Clean Cn1cc(cn1)Oc2c(cncn2)Cl
K3V RCSB PDB Q9UKK9 206.2 Da LogP 0.94 TPSA 64.2 ✓ Ro5 ✓ Clean COc1ccc2c(c1OC)C(=O)NN=C2
K41 RCSB PDB Q9UKK9 169.2 Da LogP -0.20 TPSA 72.7 ✓ Ro5 ✓ Clean CC(C)C(=O)Nc1nnn(n1)C
PG0 RCSB PDB Q6MIH8 120.1 Da LogP -0.36 TPSA 38.7 ✓ Ro5 ✓ Clean COCCOCCO
PW7 RCSB PDB Q9UKK9 163.1 Da LogP 1.08 TPSA 51.8 ✓ Ro5 ✓ Clean c1cnc(nc1C(F)(F)F)N
PWA RCSB PDB Q9UKK9 164.1 Da LogP 1.06 TPSA 45.8 ✓ Ro5 ✓ Clean c1cc2c(cc1F)N=CNC2=O
PWD RCSB PDB Q9UKK9 136.1 Da LogP 1.70 TPSA 28.7 ✓ Ro5 ✓ Clean c1c[nH]c2c1cc(cn2)F
PWG RCSB PDB Q9UKK9 237.1 Da LogP 2.69 TPSA 30.2 ✓ Ro5 ✓ Clean c1cc(c2nnc(n2c1)C(F)F)C(F)(F)F
PWJ RCSB PDB Q9UKK9 245.6 Da LogP 2.88 TPSA 41.1 ✓ Ro5 ✓ Clean c1cn2cc(c(c(c2n1)Cl)C#N)C(F)(F)F
PWM RCSB PDB Q9UKK9 164.1 Da LogP 1.06 TPSA 45.8 ✓ Ro5 ✓ Clean c1cc2c(c(c1)F)C(=O)NC=N2
PWP RCSB PDB Q9UKK9 164.1 Da LogP 1.06 TPSA 45.8 ✓ Ro5 ✓ Clean c1cc2c(cc1F)C(=O)NC=N2
PWS RCSB PDB Q9UKK9 224.2 Da LogP 1.52 TPSA 34.9 ✓ Ro5 ✓ Clean CN1C(=O)C=C(N=C1SC)C(F)(F)F
R5P RCSB PDB Q84CU3 230.1 Da LogP -2.62 TPSA 144.5 ✓ Ro5 ✓ Clean C(C(C(C(C=O)O)O)O)OP(=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.