Protein profile

KP13_09841

ADP compounds hydrolase nudE

Genome: KpKP13

Gene: nudE ANJ86570.1 Structure source: AlphaFold + ColabFold UniProt A0A0H3GYF3
Amino acids 186
Annotations 5
Features 12
PDB binders 54
Druggability 0.306

Overview

Basic information about this protein and its source genome.

Accession
KP13_09841
Gene
nudE ANJ86570.1
Status
annotated
Amino acids
186
Structure source
AlphaFold + ColabFold

Target profile

Computed evidence for target prioritization.

Human off-target
hit
Human identity (%)
29.907
Human E-value
9.5e-09
Gut microbiome off-target
hit
Essential (DEG)
N
DEG identity (%)
0.0
Localization
Cytoplasmic
ColabFold pLDDT
97.0

Selected Druggability evidence

AlphaFold / UniProt model

Selected Druggability is the FPocket score chosen for ranking using the curated structure priority. The 3D viewer may show a different loaded structure, so its visible pockets can differ.

FPocket 0.306
Structure A0A0H3GYF3
Pocket Pocket 10
P2Rank 0.035
Structure A0A0H3GYF3
Pocket Pocket 1
ColabFold model
FPocket 0.272 · Pocket 14
P2Rank 0.058 · Pocket 1
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 157 / 4744 genomes with a hit
Normalized 0.033

Sequence

Primary amino-acid sequence viewer.

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

5 GO

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 Features

Domain/signature hits 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; predicted models typically cover the full protein.

3D visualization script Full viewer

Loading 3D structure...

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Structural evidence

0 + 2

Experimental PDB entries and predicted models. Click Switch to display a different structure in the viewer.

Entry Method Resolution Chain Coverage Links Status
AlphaFold AF_A0A0H3GYF3
AlphaFold full sequence Viewing
ColabFold KP13_09841
ColabFold full sequence Loaded
Pocket details FPocket · P2Rank — toggle visibility and zoom from here, or open full viewer

Pockets (FPOCKET)

Showing top-ranked FPocket candidates by druggability. Druggability is color-coded: high (0.7 or higher), medium (0.4 to 0.69), low (below 0.4).

FPOCKET Sticks Spheres Surfaces Druggability Labels Zoom Positions
10 0.306

Pockets (P2RANK)

Showing top-ranked P2Rank candidates by probability. Probability is color-coded per P2Rank calibration: high (≥ 0.5), medium (0.2 – 0.49), low (< 0.2).

P2RANK Sticks Spheres Surfaces Score Probability Labels Zoom Positions
1 1.42 0.018
2 0.69 0.001

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

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 Q9UKK9 229.3 Da LogP 0.84 TPSA 72.5 ✓ Ro5 ✓ Clean COC(=O)c1cccc(c1)NS(=O)(=O)C
8DD 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 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 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 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 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 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 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 Q9UKK9 240.3 Da LogP 1.35 TPSA 23.6 ✓ Ro5 ✓ Clean CN1CCN(CC1)C(=O)c2ccc(c(c2)F)F
GQJ Q9UKK9 239.2 Da LogP 0.03 TPSA 80.0 ✓ Ro5 ✓ Clean COC(=O)[C@@H]1C[C@H](CN1C(=O)c2ccco2)O
JH4 Q9UKK9 109.1 Da LogP 0.52 TPSA 37.8 ✓ Ro5 ✓ Clean CNc1ncccn1
JJM Q9UKK9 239.3 Da LogP 2.42 TPSA 55.6 ✓ Ro5 ✓ Clean Cc1cccc(c1)Nc2c3cnn(c3ncn2)C
JMM Q9UKK9 248.3 Da LogP 0.97 TPSA 53.8 ✓ Ro5 ✓ Clean c1cc(oc1)C(=O)N2CCN(CC2)C(=O)C3CC3
K04 Q9UKK9 213.3 Da LogP 0.90 TPSA 64.1 ✓ Ro5 ✓ Clean C[C@H]1CCO[C@@H]1C(=O)Nc2cnns2
K07 Q9UKK9 227.7 Da LogP 1.60 TPSA 38.2 ✓ Ro5 ✓ Clean CN(C[C@H]1CCOC1)c2c(cncn2)Cl
K0A Q9UKK9 210.3 Da LogP 2.00 TPSA 33.2 ✓ Ro5 ✓ Clean Cc1c(nc(s1)C)C(=O)N2CCCC2
K0D Q9UKK9 227.3 Da LogP 0.79 TPSA 55.3 ✓ Ro5 ✓ Clean C[C@@H]1CN([C@H](CO1)C)C(=O)c2cnsn2
K0G Q9UKK9 213.2 Da LogP 2.73 TPSA 54.0 ✓ Ro5 ✓ Clean c1ccc(cc1)NC(=O)Nc2cccnc2
K0J Q9UKK9 140.1 Da LogP -0.45 TPSA 70.7 ✓ Ro5 ✓ Clean CCNC(=O)c1c[nH]nn1
K0M Q9UKK9 206.2 Da LogP 0.97 TPSA 73.0 ✓ Ro5 ✓ Clean Cc1cc(on1)C(=O)Nc2ccn(n2)C
K0P Q9UKK9 230.3 Da LogP 1.23 TPSA 59.8 ✓ Ro5 ✓ Clean CCn1cc(cn1)CNC(=O)c2cccnc2
K0S Q9UKK9 248.3 Da LogP 2.14 TPSA 67.8 ✓ Ro5 ✓ Clean CCCc1nnc(s1)NC(=O)c2ccccn2
K0V Q9UKK9 242.3 Da LogP 1.38 TPSA 58.6 ✓ Ro5 ✓ Clean CC(C)(C)NC(=O)N1CCC(CC1)C(=O)OC
K0Y Q9UKK9 198.2 Da LogP -0.11 TPSA 81.4 ✓ Ro5 ✓ Clean Cc1cc(no1)C(=O)NCC(=O)OC
K1A Q9UKK9 225.3 Da LogP 1.27 TPSA 60.9 ✓ Ro5 ✓ Clean Cc1c(c(on1)C)CN2C(=O)SC(=N2)C
K1D Q9UKK9 175.2 Da LogP 0.56 TPSA 57.7 ✓ Ro5 ✓ Clean c1[nH]c2c(n1)c(ncn2)N3CCC3
K1G Q9UKK9 205.3 Da LogP 1.21 TPSA 46.8 ✓ Ro5 ✓ Clean CC(C)N(C)c1c2cnn(c2ncn1)C
K1S Q9UKK9 205.3 Da LogP 1.28 TPSA 46.3 ✓ Ro5 ✓ Clean CCN(CC)c1cc(nc2n1ncn2)C
K1V Q9UKK9 170.2 Da LogP -0.27 TPSA 63.4 ✓ Ro5 ✓ Clean CC(=O)N1CCC[C@H](C1)C(=O)N
K1Y Q9UKK9 248.3 Da LogP 3.30 TPSA 51.2 ✓ Ro5 ✓ Clean Cc1nc(c(s1)NC(=O)OC)c2ccccc2
K24 Q9UKK9 156.2 Da LogP 0.81 TPSA 42.0 ✓ Ro5 ✓ Clean Cc1ncc(s1)C(=O)NC
K2J Q9UKK9 139.2 Da LogP 0.53 TPSA 47.0 ✓ Ro5 ✓ Clean CNc1nccc(n1)OC
K2M Q9UKK9 223.2 Da LogP 0.12 TPSA 79.8 ✓ Ro5 ✓ Clean c1cc(oc1)C(=O)N2CCN(CC2)C(=O)N
K2P Q9UKK9 206.1 Da LogP 2.28 TPSA 46.5 ✓ Ro5 ✓ Clean c1ccc(c(c1)C(=O)O)OC(F)(F)F
K2S 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 Q9UKK9 199.3 Da LogP 2.16 TPSA 51.8 ✓ Ro5 ✓ Clean C[C@H](c1ccc(cc1)c2cncnc2)N
K31 Q9UKK9 187.2 Da LogP 2.28 TPSA 54.7 ✓ Ro5 ✓ Clean Cc1c(c(n[nH]1)C)c2ccccc2N
K34 Q9UKK9 152.2 Da LogP 0.93 TPSA 54.5 ✓ Ro5 ✓ Clean c1csc(n1)c2[nH]ncn2
K3A Q9UKK9 139.2 Da LogP 0.68 TPSA 57.8 ✓ Ro5 ✓ Clean Cc1cc(n[nH]1)NC(=O)C
K3D Q9UKK9 199.3 Da LogP -0.12 TPSA 52.7 ✓ Ro5 ✓ Clean CCNC(=O)N1CCN(CC1)C(=O)C
K3J Q9UKK9 137.2 Da LogP 1.22 TPSA 37.8 ✓ Ro5 ✓ Clean CCNc1ccc(nn1)C
K3P Q9UKK9 210.6 Da LogP 1.66 TPSA 52.8 ✓ Ro5 ✓ Clean Cn1cc(cn1)Oc2c(cncn2)Cl
K3V Q9UKK9 206.2 Da LogP 0.94 TPSA 64.2 ✓ Ro5 ✓ Clean COc1ccc2c(c1OC)C(=O)NN=C2
K41 Q9UKK9 169.2 Da LogP -0.20 TPSA 72.7 ✓ Ro5 ✓ Clean CC(C)C(=O)Nc1nnn(n1)C
PG0 Q6MIH8 120.1 Da LogP -0.36 TPSA 38.7 ✓ Ro5 ✓ Clean COCCOCCO
PW7 Q9UKK9 163.1 Da LogP 1.08 TPSA 51.8 ✓ Ro5 ✓ Clean c1cnc(nc1C(F)(F)F)N
PWA Q9UKK9 164.1 Da LogP 1.06 TPSA 45.8 ✓ Ro5 ✓ Clean c1cc2c(cc1F)N=CNC2=O
PWD Q9UKK9 136.1 Da LogP 1.70 TPSA 28.7 ✓ Ro5 ✓ Clean c1c[nH]c2c1cc(cn2)F
PWG Q9UKK9 237.1 Da LogP 2.69 TPSA 30.2 ✓ Ro5 ✓ Clean c1cc(c2nnc(n2c1)C(F)F)C(F)(F)F
PWJ Q9UKK9 245.6 Da LogP 2.88 TPSA 41.1 ✓ Ro5 ✓ Clean c1cn2cc(c(c(c2n1)Cl)C#N)C(F)(F)F
PWM Q9UKK9 164.1 Da LogP 1.06 TPSA 45.8 ✓ Ro5 ✓ Clean c1cc2c(c(c1)F)C(=O)NC=N2
PWP Q9UKK9 164.1 Da LogP 1.06 TPSA 45.8 ✓ Ro5 ✓ Clean c1cc2c(cc1F)C(=O)NC=N2
PWS Q9UKK9 224.2 Da LogP 1.52 TPSA 34.9 ✓ Ro5 ✓ Clean CN1C(=O)C=C(N=C1SC)C(F)(F)F
R5P 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.