Protein profile

PA0439

dihydropyrimidine dehydrogenase

Genome: NC_002516.2

Gene: PA0439 Structure source: AlphaFold UniProt Q9I678
Amino acids 425
Annotations 6
Features 20
PDB binders 59
Druggability 0.582

Overview

Basic information about this protein and its source genome.

Accession
PA0439
Gene
PA0439
Status
annotated
Amino acids
425
Structure source
AlphaFold

Target profile

Computed evidence for target prioritization.

Human off-target
hit
Human identity (%)
37.092
Human E-value
5.47e-61
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 0.582
Structure
Pocket

Sequence

Primary amino-acid sequence viewer.

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 5 GO

Enzyme Commission (EC)

1

Gene Ontology (GO)

5
  • GO:0005737 The contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
  • GO:0004159 Catalysis of the reaction: a 5,6-dihydropyrimidine (5,6-dihydrouracil or 5,6-dihydrothymine) + NAD+ = a pyrimidine (uracil or thymine) + NADH + H+.
  • GO:0051536 Binding to an iron-sulfur cluster, a combination of iron and sulfur atoms.
  • GO:0046872 Binding to a metal ion.
  • GO:0016627 Catalysis of an oxidation-reduction (redox) reaction in which a CH-CH group acts as a hydrogen or electron donor and reduces a hydrogen or electron acceptor.

Sequence Features

Domain/signature hits from InterPro and related databases.

20 records
Show feature table
Start End DB Term Name
309 412 FunFam G3DSA:3.30.70.20:FF:000087 NAD-dependent dihydropyrimidine dehydrogenase subunit PreA
4 302 CDD cd02940 DHPD_FMN
383 394 ProSitePatterns PS00198 4Fe-4S ferredoxin-type iron-sulfur binding region signature.
383 394 InterPro IPR017900 4Fe-4S ferredoxin, iron-sulphur binding, conserved site
5 311 Gene3D G3DSA:3.20.20.70 Aldolase class I
5 311 InterPro IPR013785 Aldolase-type TIM barrel
5 306 Pfam PF01180 Dihydroorotate dehydrogenase
5 306 InterPro IPR005720 Dihydroorotate dehydrogenase domain
308 408 PANTHER PTHR43073 DIHYDROPYRIMIDINE DEHYDROGENASE [NADP(+)]
337 366 ProSiteProfiles PS51379 4Fe-4S ferredoxin-type iron-sulfur binding domain profile.
337 366 InterPro IPR017896 4Fe-4S ferredoxin-type, iron-sulphur binding domain
5 312 FunFam G3DSA:3.20.20.70:FF:000027 Dihydropyrimidine dehydrogenase [NADP(+)]
5 320 NCBIfam TIGR01037 dihydroorotate dehydrogenase family protein
5 320 InterPro IPR005720 Dihydroorotate dehydrogenase domain
374 404 ProSiteProfiles PS51379 4Fe-4S ferredoxin-type iron-sulfur binding domain profile.
374 404 InterPro IPR017896 4Fe-4S ferredoxin-type, iron-sulphur binding domain
339 401 Pfam PF14697 4Fe-4S dicluster domain
318 402 SUPERFAMILY SSF54862 4Fe-4S ferredoxins
2 320 SUPERFAMILY SSF51395 FMN-linked oxidoreductases
317 415 Gene3D G3DSA:3.30.70.20 -

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

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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 PA0439
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
1 0.582

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
2RO Q4D3W2 316.4 Da LogP 1.84 TPSA 103.0 ✓ Ro5 ✓ Clean CC(C)(C)c1ccc(cc1)CCC2=C(NC(=O)NC2=O)C(=O)O
3RO Q4D3W2 294.7 Da LogP 1.20 TPSA 103.0 ✓ Ro5 ✓ Clean c1cc(cc(c1)Cl)CCC2=C(NC(=O)NC2=O)C(=O)O
5LL Q4D3W2 232.2 Da LogP 0.59 TPSA 88.4 ✓ Ro5 Alert c1cc(oc1)/C=C/C=C2C(=O)NC(=O)NC2=O
5LM Q4D3W2 248.3 Da LogP 1.05 TPSA 75.3 ✓ Ro5 Alert c1cc(sc1)/C=C/C=C2C(=O)NC(=O)NC2=O
CAC Q4D3W2 137.0 Da LogP -0.52 TPSA 40.1 ✓ Ro5 ✓ Clean C[As](=O)(C)[O-]
DOR Q4D3W2 158.1 Da LogP -1.33 TPSA 95.5 ✓ Ro5 ✓ Clean C1[C@H](NC(=O)NC1=O)C(=O)O
ERO Q4D3W2 182.1 Da LogP -0.60 TPSA 103.0 ✓ Ro5 ✓ Clean C=CC1=C(NC(=O)NC1=O)C(=O)O
FES P54322 175.8 Da LogP 1.29 TPSA 0.0 ✓ Ro5 ✓ Clean S1[Fe]S[Fe]1
FOT Q4D3W2 174.1 Da LogP -1.10 TPSA 103.0 ✓ Ro5 ✓ Clean C1(=C(NC(=O)NC1=O)C(=O)O)F
FUM Q4D3W2 116.1 Da LogP -0.29 TPSA 74.6 ✓ Ro5 ✓ Clean C(=C/C(=O)O)\C(=O)O
HRO Q4D3W2 190.5 Da LogP -0.59 TPSA 103.0 ✓ Ro5 ✓ Clean C1(=C(NC(=O)NC1=O)C(=O)O)Cl
IRO Q4D3W2 282.0 Da LogP -0.63 TPSA 103.0 ✓ Ro5 ✓ Clean C1(=C(NC(=O)NC1=O)C(=O)O)I
JDB Q4D3W2 340.3 Da LogP 1.71 TPSA 112.3 ✓ Ro5 ✓ Clean COc1ccc2ccc(cc2c1)CCC3=C(NC(=O)NC3=O)C(=O)O
JDM Q4D3W2 290.3 Da LogP 0.04 TPSA 123.2 ✓ Ro5 ✓ Clean c1ccc(c(c1)CCC2=C(NC(=O)NC2=O)C(=O)O)CO
KRO Q4D3W2 292.3 Da LogP 0.99 TPSA 103.0 ✓ Ro5 ✓ Clean Cc1cc(ccc1F)CCC2=C(NC(=O)NC2=O)C(=O)O
LRO Q4D3W2 274.3 Da LogP 0.86 TPSA 103.0 ✓ Ro5 ✓ Clean Cc1ccc(cc1)CCC2=C(NC(=O)NC2=O)C(=O)O
MLI Q57U83 102.0 Da LogP -3.12 TPSA 80.3 ✓ Ro5 ✓ Clean C(C(=O)[O-])C(=O)[O-]
MRO Q4D3W2 260.2 Da LogP 0.55 TPSA 103.0 ✓ Ro5 ✓ Clean c1ccc(cc1)CCC2=C(NC(=O)NC2=O)C(=O)O
ORO A2RJT9 156.1 Da LogP -1.24 TPSA 103.0 ✓ Ro5 ✓ Clean C1=C(NC(=O)NC1=O)C(=O)O
OXC Q4D3W2 159.1 Da LogP -1.58 TPSA 107.5 ✓ Ro5 ✓ Clean C1(NC(=O)NC(=O)N1)C(=O)O
QRO Q4D3W2 296.2 Da LogP 0.82 TPSA 103.0 ✓ Ro5 ✓ Clean c1cc(c(cc1CCC2=C(NC(=O)NC2=O)C(=O)O)F)F
ROD Q4D3W2 328.2 Da LogP 1.57 TPSA 103.0 ✓ Ro5 ✓ Clean c1ccc(c(c1)CCC2=C(NC(=O)NC2=O)C(=O)O)C(F)(F)F
ROE Q4D3W2 340.3 Da LogP 1.71 TPSA 112.3 ✓ Ro5 ✓ Clean COc1ccc2cc(ccc2c1)CCC3=C(NC(=O)NC3=O)C(=O)O
ROU Q4D3W2 396.2 Da LogP 2.58 TPSA 103.0 ✓ Ro5 ✓ Clean c1c(cc(cc1C(F)(F)F)C(F)(F)F)CCC2=C(NC(=O)NC2=O)…
RRO Q4D3W2 235.0 Da LogP -0.48 TPSA 103.0 ✓ Ro5 ✓ Clean C1(=C(NC(=O)NC1=O)C(=O)O)Br
SIN Q4D3W2 118.1 Da LogP -0.06 TPSA 74.6 ✓ Ro5 ✓ Clean C(CC(=O)O)C(=O)O
VRO Q4D3W2 290.3 Da LogP 0.56 TPSA 112.3 ✓ Ro5 ✓ Clean COc1ccc(cc1)CCC2=C(NC(=O)NC2=O)C(=O)O
W6Y Q4D3W2 354.3 Da LogP 1.40 TPSA 140.3 ✓ Ro5 ✓ Clean c1cc2cc(ccc2c(c1)C(=O)O)CCC3=C(NC(=O)NC3=O)C(=O…
W70 Q4D3W2 352.3 Da LogP 2.34 TPSA 112.3 ✓ Ro5 ✓ Clean c1ccc(cc1)Oc2ccc(cc2)CCC3=C(NC(=O)NC3=O)C(=O)O
W73 Q4D3W2 360.4 Da LogP 2.85 TPSA 103.0 ✓ Ro5 ✓ Clean c1ccc2c(c1)cc(c3c2cccc3)CCC4=C(NC(=O)NC4=O)C(=O…
W74 Q4D3W2 344.2 Da LogP 1.45 TPSA 112.2 ✓ Ro5 ✓ Clean c1cc(ccc1CCC2=C(NC(=O)NC2=O)C(=O)O)OC(F)(F)F
W75 Q4D3W2 320.3 Da LogP 0.56 TPSA 121.5 ✓ Ro5 ✓ Clean COc1cc(cc(c1)OC)CCC2=C(NC(=O)NC2=O)C(=O)O
W76 Q4D3W2 290.3 Da LogP 0.56 TPSA 112.3 ✓ Ro5 ✓ Clean COc1cccc(c1)CCC2=C(NC(=O)NC2=O)C(=O)O
W7A Q4D3W2 336.3 Da LogP 2.21 TPSA 103.0 ✓ Ro5 ✓ Clean c1ccc(cc1)c2ccc(cc2)CCC3=C(NC(=O)NC3=O)C(=O)O
W7B Q4D3W2 310.3 Da LogP 1.70 TPSA 103.0 ✓ Ro5 ✓ Clean c1ccc2c(c1)cccc2CCC3=C(NC(=O)NC3=O)C(=O)O
W7C Q4D3W2 340.3 Da LogP 1.71 TPSA 112.3 ✓ Ro5 ✓ Clean COc1cccc2c1ccc(c2)CCC3=C(NC(=O)NC3=O)C(=O)O
W7D Q4D3W2 340.3 Da LogP 1.71 TPSA 112.3 ✓ Ro5 ✓ Clean COc1cccc2c1cc(cc2)CCC3=C(NC(=O)NC3=O)C(=O)O
W7F Q4D3W2 340.3 Da LogP 1.71 TPSA 112.3 ✓ Ro5 ✓ Clean COc1ccc2cccc(c2c1)CCC3=C(NC(=O)NC3=O)C(=O)O
W7G Q4D3W2 290.3 Da LogP 0.56 TPSA 112.3 ✓ Ro5 ✓ Clean COc1ccccc1CCC2=C(NC(=O)NC2=O)C(=O)O
W7H Q4D3W2 310.3 Da LogP 1.70 TPSA 103.0 ✓ Ro5 ✓ Clean c1ccc2cc(ccc2c1)CCC3=C(NC(=O)NC3=O)C(=O)O
W7I Q4D3W2 340.3 Da LogP 1.71 TPSA 112.3 ✓ Ro5 ✓ Clean COc1cc2ccccc2cc1CCC3=C(NC(=O)NC3=O)C(=O)O
W7J Q4D3W2 354.3 Da LogP 1.40 TPSA 140.3 ✓ Ro5 ✓ Clean c1cc2cc(ccc2cc1CCC3=C(NC(=O)NC3=O)C(=O)O)C(=O)O
W7K Q4D3W2 370.4 Da LogP 1.72 TPSA 121.5 ✓ Ro5 ✓ Clean COc1ccc2cc(c(cc2c1)OC)CCC3=C(NC(=O)NC3=O)C(=O)O
W7L Q4D3W2 340.3 Da LogP 1.71 TPSA 112.3 ✓ Ro5 ✓ Clean COc1ccc2c(c1)cccc2CCC3=C(NC(=O)NC3=O)C(=O)O
W7M Q4D3W2 368.3 Da LogP 1.49 TPSA 129.3 ✓ Ro5 ✓ Clean COC(=O)c1ccc2cc(ccc2c1)CCC3=C(NC(=O)NC3=O)C(=O)O
W7N Q4D3W2 397.4 Da LogP 0.42 TPSA 152.3 ✓ Ro5 ✓ Clean c1cc2cc(ccc2cc1CCC3=C(NC(=O)NC3=O)C(=O)O)C(=O)N…
W7O Q4D3W2 304.3 Da LogP 0.24 TPSA 140.3 ✓ Ro5 ✓ Clean c1cc(cc(c1)C(=O)O)CCC2=C(NC(=O)NC2=O)C(=O)O
W7P Q4D3W2 304.3 Da LogP 0.24 TPSA 140.3 ✓ Ro5 ✓ Clean c1cc(ccc1CCC2=C(NC(=O)NC2=O)C(=O)O)C(=O)O
W7Q Q4D3W2 401.4 Da LogP 1.84 TPSA 132.6 ✓ Ro5 ✓ Clean CC(C)(C)OC(=O)N1CCc2c1ccc(c2)CCC3=C(NC(=O)NC3=O…
W83 Q4D3W2 370.4 Da LogP 1.68 TPSA 121.5 ✓ Ro5 ✓ Clean COCOc1ccc2ccc(cc2c1)CCC3=C(NC(=O)NC3=O)C(=O)O
W85 Q4D3W2 318.3 Da LogP 0.33 TPSA 129.3 ✓ Ro5 ✓ Clean COC(=O)c1cccc(c1)CCC2=C(NC(=O)NC2=O)C(=O)O
W86 Q4D3W2 346.3 Da LogP 1.11 TPSA 129.3 ✓ Ro5 ✓ Clean COC(=O)c1ccc(cc1)CCCCC2=C(NC(=O)NC2=O)C(=O)O
W87 Q4D3W2 396.4 Da LogP 2.27 TPSA 129.3 ✓ Ro5 ✓ Clean COC(=O)c1cccc2c1ccc(c2)CCCCC3=C(NC(=O)NC3=O)C(=…
W88 Q4D3W2 382.4 Da LogP 2.18 TPSA 140.3 ✓ Ro5 ✓ Clean c1cc2cc(ccc2cc1CCCCC3=C(NC(=O)NC3=O)C(=O)O)C(=O…
W8Z Q4D3W2 370.4 Da LogP 1.68 TPSA 121.5 ✓ Ro5 ✓ Clean COCOc1cc2ccccc2cc1CCC3=C(NC(=O)NC3=O)C(=O)O
WRO Q4D3W2 328.2 Da LogP 1.57 TPSA 103.0 ✓ Ro5 ✓ Clean c1cc(cc(c1)C(F)(F)F)CCC2=C(NC(=O)NC2=O)C(=O)O
XRO Q4D3W2 299.3 Da LogP 0.61 TPSA 126.8 ✓ Ro5 ✓ Clean c1cc(ccc1CCC2=C(NC(=O)NC2=O)C(=O)O)CC#N
YRO Q4D3W2 240.3 Da LogP 0.74 TPSA 103.0 ✓ Ro5 ✓ Clean CC(C)(C)CCC1=C(NC(=O)NC1=O)C(=O)O
ZRO Q4D3W2 328.2 Da LogP 1.57 TPSA 103.0 ✓ Ro5 ✓ Clean c1cc(ccc1CCC2=C(NC(=O)NC2=O)C(=O)O)C(F)(F)F

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.