Protein profile

PA1524

xanthine dehydrogenase

Genome: NC_002516.2

Gene: PA1524 xdhA Structure source: AlphaFold UniProt Q9I3I9
Amino acids 484
Annotations 8
Features 39
PDB binders 23
Druggability 0.322

Overview

Basic information about this protein and its source genome.

Accession
PA1524
Gene
PA1524 xdhA
Status
annotated
Amino acids
484
Structure source
AlphaFold

Target profile

Computed evidence for target prioritization.

Human off-target
hit
Human identity (%)
47.059
Human E-value
6.4300000000000006e-27
Gut microbiome off-target
hit
Essential (DEG)
N
Localization
Cytoplasmic

Selected Druggability evidence

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 0.322
Structure
Pocket

Sequence

Primary amino-acid sequence viewer.

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

8 GO

Gene Ontology (GO)

8
  • GO:0051537 Binding to a 2 iron, 2 sulfur (2Fe-2S) cluster; this cluster consists of two iron atoms, with two inorganic sulfur atoms found between the irons and acting as bridging ligands.
  • GO:0071949 Binding to the oxidized form, FAD, of flavin-adenine dinucleotide, the coenzyme or the prosthetic group of various flavoprotein oxidoreductase enzymes.
  • GO:0005506 Binding to an iron (Fe) ion.
  • GO:0004854 Catalysis of the reaction: xanthine + NAD+ + H2O = urate + NADH + H+.
  • 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:0051536 Binding to an iron-sulfur cluster, a combination of iron and sulfur atoms.
  • 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.

Sequence Features

Domain/signature hits from InterPro and related databases.

39 records
Show feature table
Start End DB Term Name
366 475 Gene3D G3DSA:3.30.390.50 -
13 76 Pfam PF00111 2Fe-2S iron-sulfur cluster binding domain
13 76 InterPro IPR001041 2Fe-2S ferredoxin-type iron-sulfur binding domain
2 470 NCBIfam TIGR02963 xanthine dehydrogenase small subunit
2 470 InterPro IPR014307 Xanthine dehydrogenase, small subunit
248 362 Gene3D G3DSA:3.30.465.10 -
248 362 InterPro IPR016169 FAD-binding, type PCMH, subdomain 2
3 90 SUPERFAMILY SSF54292 2Fe-2S ferredoxin-like
3 90 InterPro IPR036010 2Fe-2S ferredoxin-like superfamily
368 473 SUPERFAMILY SSF55447 CO dehydrogenase flavoprotein C-terminal domain-like
368 473 InterPro IPR036683 CO dehydrogenase flavoprotein, C-terminal domain superfamily
192 365 ProSiteProfiles PS51387 PCMH-type FAD-binding domain profile.
192 365 InterPro IPR016166 FAD-binding domain, PCMH-type
1 90 ProSiteProfiles PS51085 2Fe-2S ferredoxin-type iron-sulfur binding domain profile.
1 90 InterPro IPR001041 2Fe-2S ferredoxin-type iron-sulfur binding domain
39 47 ProSitePatterns PS00197 2Fe-2S ferredoxin-type iron-sulfur binding region signature.
39 47 InterPro IPR006058 2Fe-2S ferredoxin, iron-sulphur binding site
4 471 PANTHER PTHR11908 XANTHINE DEHYDROGENASE
4 471 InterPro IPR016208 Aldehyde oxidase/xanthine dehydrogenase
201 247 Gene3D G3DSA:3.30.43.10 -
201 247 InterPro IPR016167 FAD-binding, type PCMH, subdomain 1
370 471 Pfam PF03450 CO dehydrogenase flavoprotein C-terminal domain
370 471 InterPro IPR005107 CO dehydrogenase flavoprotein, C-terminal
1 89 Gene3D G3DSA:3.10.20.30 -
1 89 InterPro IPR012675 Beta-grasp domain superfamily
90 195 Gene3D G3DSA:1.10.150.120 -
199 362 Pfam PF00941 FAD binding domain in molybdopterin dehydrogenase
199 362 InterPro IPR002346 Molybdopterin dehydrogenase, FAD-binding
184 361 SUPERFAMILY SSF56176 FAD-binding/transporter-associated domain-like
184 361 InterPro IPR036318 FAD-binding, type PCMH-like superfamily
1 484 PIRSF PIRSF036557 XdhA_RC
1 484 InterPro IPR012175 Xanthine dehydrogenase, small subunit, bacteria
97 201 SUPERFAMILY SSF47741 CO dehydrogenase ISP C-domain like
97 201 InterPro IPR036884 [2Fe-2S]-binding domain superfamily
2 77 CDD cd00207 fer2
2 77 InterPro IPR001041 2Fe-2S ferredoxin-type iron-sulfur binding domain
370 471 SMART SM01092 CO_deh_flav_C_2
86 158 Pfam PF01799 [2Fe-2S] binding domain
86 158 InterPro IPR002888 [2Fe-2S]-binding

3D Structure

Selected loaded structure. Experimental PDB entries may cover only a portion of the sequence; predicted models typically cover the full protein.

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Structural evidence

0 + 1

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

Entry Method Resolution Chain Coverage Links Status
AlphaFold PA1524
AlphaFold full sequence Viewing
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
6 0.322
1 0.218

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.

173 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
141 O54050 152.1 Da LogP -1.11 TPSA 94.4 ✓ Ro5 ✓ Clean C1=C2C(=NC(=O)NC2=O)NN1
290 P80457 150.1 Da LogP -0.05 TPSA 74.4 ✓ Ro5 ✓ Clean CC1=NC(=O)Nc2c1nc[nH]2
FES P80457 175.8 Da LogP 1.29 TPSA 0.0 ✓ Ro5 ✓ Clean S1[Fe]S[Fe]1
FYO P80457 296.2 Da LogP -0.54 TPSA 144.4 ✓ Ro5 ✓ Clean C1C(=CC(=O)NC1=O)c2[nH]nc(n2)C3=CC(=O)NC(=C3)C#N
FYX P80457 248.2 Da LogP 1.80 TPSA 91.1 ✓ Ro5 ✓ Clean c1cnccc1c2[nH]nc(n2)c3ccnc(c3)C#N
GUN P80457 151.1 Da LogP -0.77 TPSA 100.5 ✓ Ro5 ✓ Clean c1[nH]c2c(n1)C(=O)NC(=N2)N
HHR O54050 193.2 Da LogP -1.21 TPSA 117.8 ✓ Ro5 ✓ Clean c1c(nc2c(n1)N=C(NC2=O)N)CO
HPA P80457 136.1 Da LogP -0.35 TPSA 74.4 ✓ Ro5 ✓ Clean c1[nH]c2c(n1)N=CNC2=O
I3A P80457 145.2 Da LogP 1.98 TPSA 32.9 ✓ Ro5 ✓ Clean c1ccc2c(c1)c(c[nH]2)C=O
LUZ P80457 164.1 Da LogP -0.99 TPSA 91.5 ✓ Ro5 ✓ Clean c1cnc2c(n1)C(=O)NC(=O)N2
LZU Q06278 370.6 Da LogP 5.89 TPSA 6.5 1 viol. ✓ Clean CN1CCCC[C@H]1CCN2c3ccccc3Sc4c2cc(cc4)SC
MLI Q06278 102.0 Da LogP -3.12 TPSA 80.3 ✓ Ro5 ✓ Clean C(C(=O)[O-])C(=O)[O-]
MOM P80457 144.9 Da LogP -0.80 TPSA 54.4 ✓ Ro5 ✓ Clean O[Mo](=O)=O
MOS Q06278 161.0 Da LogP 0.14 TPSA 34.1 ✓ Ro5 ✓ Clean O=[Mo](=O)S
MTE P80457 395.4 Da LogP -0.54 TPSA 171.8 1 viol. ✓ Clean C([C@@H]1C(=C([C@H]2[C@@H](O1)NC3=C(N2)C(=O)NC(…
PM6 P80457 152.2 Da LogP 0.64 TPSA 54.5 ✓ Ro5 ✓ Clean c1[nH]c2c(n1)c(ncn2)S
QUE P80457 302.2 Da LogP 1.99 TPSA 131.4 ✓ Ro5 Alert c1cc(c(cc1C2=C(C(=O)c3c(cc(cc3O2)O)O)O)O)O
RMO P80457 251.9 Da LogP -0.48 TPSA 46.5 ✓ Ro5 ✓ Clean O[As]1O[Mo](=O)S1
SAL P80457 138.1 Da LogP 1.09 TPSA 57.5 ✓ Ro5 ✓ Clean c1ccc(c(c1)C(=O)O)O
TEI P80457 316.4 Da LogP 3.72 TPSA 83.2 ✓ Ro5 ✓ Clean Cc1c(sc(n1)c2ccc(c(c2)C#N)OCC(C)C)C(=O)O
XAN P80457 152.1 Da LogP -1.06 TPSA 94.4 ✓ Ro5 ✓ Clean c1[nH]c2c(n1)C(=O)NC(=O)N2
XAX P80457 554.4 Da LogP -0.03 TPSA 209.1 3 viol. ✓ Clean C([C@@H]1C2=C([C@H]3[C@@H](O1)NC4=C(N3)C(=O)NC(…
YSH P80457 299.3 Da LogP 2.87 TPSA 88.1 ✓ Ro5 ✓ Clean CC(C)(C)COc1ccc(cc1C#N)n2cc(cn2)C(=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.