Protein profile

PA3050

dihydroorotate dehydrogenase

Genome: NC_002516.2

Gene: PA3050 pyrD Structure source: AlphaFold UniProt Q9HZF8
Amino acids 342
Annotations 11
Features 17
PDB binders 76
Druggability 0.756

Overview

Basic information about this protein and its source genome.

Accession
PA3050
Gene
PA3050 pyrD
Status
annotated
Amino acids
342
Structure source
AlphaFold

Target profile

Computed evidence for target prioritization.

Human off-target
hit
Human identity (%)
50.413
Human E-value
6.37e-35
Gut microbiome off-target
hit
Essential (DEG)
Y
Localization
CytoplasmicMembrane

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 0.756
Structure
Pocket

Sequence

Primary amino-acid sequence viewer.

MYTLARQLLFKLSPETSHELSIDLIGAGGRLGLNRLLTPKPASLPVSVLGLEFPNPVGLAAGLDKNGDAIDGFGQLGFGFIEIGTVTPRPQPGNPRPRLFRLPQANAIINRMGFNNHGVDHLLARVRAAKYRGVLGINIGKNFDTPVERAVDDYLICLDKVYADASYVTVNVSSPNTPGLRSLQFGDSLKQLLEALRQRQEALALRHGRRVPLAIKIAPDMTDEETALVAAALVEAGMDAVIATNTTLGREGVEGLPHGDEAGGLSGAPVREKSTHTVKVLAGELGGRLPIIAAGGITEGAHAAEKIAAGASLVQIYSGFIYKGPALIREAVDAIAALPRRN

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:0005737 The contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
  • GO:0005886 The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.
  • GO:0106430 (S)-dihydroorotate + a quinone = orotate + a quinol.
  • GO:0004152 Catalysis of the reaction: (S)-dihydroorotate + A = AH(2) + orotate.
  • GO:0006207 The chemical reactions and pathways resulting in the formation of pyrimidine nucleobases, 1,3-diazine, organic nitrogenous bases, beginning with the synthesis of a pyrimidine ring from simpler precursors.
  • GO:0044205 The chemical reactions and pathways resulting in the formation of UMP, uridine monophosphate, starting with the synthesis of (S)-dihydroorotate from bicarbonate; UMP biosynthesis may either occur via reduction by quinone, NAD+ or oxygen.
  • GO:0009220 The chemical reactions and pathways resulting in the formation of a pyrimidine ribonucleotide, a compound consisting of nucleoside (a pyrimidine base linked to a ribose sugar) esterified with a phosphate group at either the 3' or 5'-hydroxyl group of the sugar.
  • 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.
  • GO:0016020 A lipid bilayer along with all the proteins and protein complexes embedded in it and attached to it.
  • GO:0006222 The chemical reactions and pathways resulting in the formation of UMP, uridine monophosphate.

Sequence Features

Domain/signature hits from InterPro and related databases.

17 records
Show feature table
Start End DB Term Name
2 338 NCBIfam TIGR01036 dihydroorotate dehydrogenase (quinone)
2 338 InterPro IPR005719 Dihydroorotate dehydrogenase, class 2
6 335 CDD cd04738 DHOD_2_like
6 335 InterPro IPR005719 Dihydroorotate dehydrogenase, class 2
79 98 ProSitePatterns PS00911 Dihydroorotate dehydrogenase signature 1.
79 98 InterPro IPR001295 Dihydroorotate dehydrogenase, conserved site
5 338 PANTHER PTHR48109 DIHYDROOROTATE DEHYDROGENASE (QUINONE), MITOCHONDRIAL-RELATED
1 334 Gene3D G3DSA:3.20.20.70 Aldolase class I
1 334 InterPro IPR013785 Aldolase-type TIM barrel
1 336 SUPERFAMILY SSF51395 FMN-linked oxidoreductases
1 335 FunFam G3DSA:3.20.20.70:FF:000028 Dihydroorotate dehydrogenase (quinone)
16 342 PIRSF PIRSF000164 DHO_oxidase
16 342 InterPro IPR012135 Dihydroorotate dehydrogenase, class 1/ 2
44 335 Pfam PF01180 Dihydroorotate dehydrogenase
44 335 InterPro IPR005720 Dihydroorotate dehydrogenase domain
1 335 Hamap MF_00225 Dihydroorotate dehydrogenase (quinone) [pyrD].
1 335 InterPro IPR005719 Dihydroorotate dehydrogenase, class 2

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 PA3050
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 0.756

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.

226 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
03U Q02127 368.4 Da LogP 3.96 TPSA 99.4 ✓ Ro5 ✓ Clean CCC(=C(C#N)C(=O)Nc1ccc(c(c1)C(=O)OC)c2ccc(cc2)F…
18X Q02127 368.4 Da LogP 3.48 TPSA 70.4 ✓ Ro5 ✓ Clean COC(=O)C(=C1N(C(=O)CS1)c2ccc(cc2F)c3ccccc3)C#N
1EA Q02127 415.5 Da LogP 6.96 TPSA 59.4 1 viol. ✓ Clean Cc1cc(c(cc1c2cc(c3cc(ccc3n2)F)C(=O)O)C(C)C)Oc4c…
1KL Q02127 449.5 Da LogP 4.22 TPSA 99.5 ✓ Ro5 ✓ Clean CC(C)(C)c1ccc(cc1)NC(=O)c2ccc(cc2)N3C(=O)CSC3=C…
1SU Q02127 554.5 Da LogP 6.65 TPSA 104.1 2 viol. ✓ Clean c1cc(cc(c1)C(F)(F)F)CC(=O)Nc2cc(ccc2F)Oc3ccc4c(…
1X5 Q02127 325.4 Da LogP 2.76 TPSA 82.5 ✓ Ro5 ✓ Clean CN(Cc1cccnc1)c2ccc(c(c2)C(=O)O)NC(=O)C3CC3
201 Q02127 317.3 Da LogP 3.82 TPSA 80.4 ✓ Ro5 ✓ Clean c1ccc(cc1)c2ccc(cc2)c3cc(cc(c3)C(=O)O)C(=O)N
238 Q02127 391.8 Da LogP 6.37 TPSA 50.2 1 viol. ✓ Clean Cc1c(c2cc(ccc2nc1c3ccc(cc3)c4ccccc4F)Cl)C(=O)O
3RV Q02127 392.4 Da LogP 4.76 TPSA 78.8 ✓ Ro5 Alert c1ccc2c(c1)cccc2/C=C\3/C(=O)N=C(S3)Nc4ccc(cc4C(…
3RY Q02127 376.4 Da LogP 3.73 TPSA 78.8 ✓ Ro5 Alert c1ccc2c(c1)cccc2CC3=SC(=NC3=O)Nc4ccccc4C(=O)O
3SH Q02127 372.9 Da LogP 5.69 TPSA 51.2 1 viol. ✓ Clean CCOC(=O)c1c(nc(s1)Nc2ccc(c(c2)Cl)C)c3ccccc3
3V1 Q02127 495.0 Da LogP 5.83 TPSA 124.3 1 viol. ✓ Clean Cc1c(sc(n1)Cl)C(=O)Nc2cccc(c2)Oc3ccc(cc3)NC(=O)…
3X2 Q02127 357.8 Da LogP 4.61 TPSA 74.6 ✓ Ro5 ✓ Clean c1ccc(c(c1)/C=N/Nc2nc(cs2)c3ccccc3Cl)C(=O)O
3XS Q02127 353.4 Da LogP 3.96 TPSA 83.8 ✓ Ro5 ✓ Clean COc1cccc(c1)c2csc(n2)N/N=C/c3ccccc3C(=O)O
4JG Q02127 282.4 Da LogP 4.55 TPSA 42.0 ✓ Ro5 ✓ Clean Cc1c(sc(n1)Nc2ccc3ccccc3c2)C(=O)C
4R5 Q02127 361.4 Da LogP 4.74 TPSA 63.2 ✓ Ro5 ✓ Clean COc1cccc(c1)c2cc(c(c(c2)F)NC(=O)Nc3cncs3)F
52Y Q02127 398.4 Da LogP 3.49 TPSA 79.6 ✓ Ro5 ✓ Clean COc1ccc(cc1)c2ccc(c(c2)F)N3C(=O)CSC3=C(C#N)C(=O…
64B Q02127 322.3 Da LogP 1.82 TPSA 79.6 ✓ Ro5 ✓ Clean COc1ccc(c(c1)F)N2C(=O)CSC2=C(C#N)C(=O)OC
6X1 Q02127 325.2 Da LogP 4.34 TPSA 78.4 ✓ Ro5 ✓ Clean c1ccc(c(c1)C(=O)O)NC(=O)Nc2cc(cc(c2)Cl)Cl
7GF Q02127 357.2 Da LogP 1.87 TPSA 72.6 ✓ Ro5 ✓ Clean COC(=O)/C(=C\1/N(C(=O)CS1)c2ccc(cc2)Br)/CN
7L7 Q02127 292.3 Da LogP 1.81 TPSA 70.4 ✓ Ro5 ✓ Clean COC(=O)C(=C1N(C(=O)CS1)c2ccccc2F)C#N
7Z5 Q02127 313.4 Da LogP 2.76 TPSA 82.5 ✓ Ro5 ✓ Clean CCC(=O)Nc1ccc(cc1C(=O)O)N(C)Cc2cccnc2
951 Q02127 340.8 Da LogP 4.74 TPSA 74.8 ✓ Ro5 Alert c1ccc(c(c1)c2ccc(o2)/C=N/Nc3ccccc3C(=O)O)Cl
9AU Q02127 366.5 Da LogP 6.46 TPSA 50.4 1 viol. ✓ Clean CC(=CCC/C(=C/CC/C(=C/CC1=C(c2ccccc2OC1=O)O)/C)/…
9BL Q02127 366.8 Da LogP 4.26 TPSA 83.8 ✓ Ro5 ✓ Clean Cc1c(c(c(c(c1Cl)O)C/C=C(\C)/CC/C=C(\C)/C(=O)OC)…
9BO Q02127 394.9 Da LogP 5.04 TPSA 83.8 1 viol. ✓ Clean Cc1c(c(c(c(c1Cl)O)C/C=C(\C)/CC/C=C(\C)/[C@H](C)…
9BR Q02127 391.0 Da LogP 6.83 TPSA 57.5 1 viol. ✓ Clean Cc1c(c(c(c(c1Cl)O)C/C=C(\C)/CC/C=C(\C)/CCC=C(C)…
9BU Q02127 408.9 Da LogP 5.29 TPSA 83.8 1 viol. ✓ Clean Cc1c(c(c(c(c1Cl)O)C/C=C(\C)/CC/C(=C/COC(=O)C(C)…
9BX Q02127 420.9 Da LogP 4.98 TPSA 94.8 ✓ Ro5 ✓ Clean Cc1c(c(c(c(c1Cl)O)C/C=C(/C)\CC/C=C(/C)\C=C\C(=O…
A26 Q02127 270.2 Da LogP 3.00 TPSA 73.1 ✓ Ro5 ✓ Clean CC(=C(C#N)C(=O)Nc1ccc(cc1)C(F)(F)F)O
AVQ Q02127 341.2 Da LogP 3.74 TPSA 63.3 ✓ Ro5 ✓ Clean Cc1cc(n2c(n1)nc(n2)SCc3cc(ccc3Cl)Cl)O
AYR Q02127 285.3 Da LogP 3.00 TPSA 38.8 ✓ Ro5 ✓ Clean c1cc2c(cc1/C=C/C=C/C(=O)N3CCCCC3)OCO2
B3B Q02127 307.4 Da LogP 4.07 TPSA 54.4 ✓ Ro5 ✓ Clean c1ccc(cc1)c2csc(n2)N/N=C/c3ccccc3C=O
B5O Q02127 415.4 Da LogP 4.25 TPSA 68.0 ✓ Ro5 ✓ Clean CC(C)[C@@H]1Cc2c(nnn2c3cc(c(c(c3)F)c4cc(ccc4F)C…
B5X Q02127 410.5 Da LogP 4.68 TPSA 51.0 ✓ Ro5 ✓ Clean CC(C)[C@@H]1Cc2c(nnn2c3cc(c(c(c3)F)c4cccc(c4)N(…
B6O Q02127 430.4 Da LogP 4.05 TPSA 68.1 ✓ Ro5 Alert CN(C)c1cccc(c1)c2c(cc(cc2F)n3c4c(nn3)C(=O)c5ccc…
B6R Q02127 417.4 Da LogP 4.00 TPSA 74.1 ✓ Ro5 Alert COc1cccc(c1)c2c(cc(cc2F)n3c4c(nn3)C(=O)c5ccccc5…
B6U Q02127 435.4 Da LogP 3.62 TPSA 85.1 ✓ Ro5 Alert c1ccc2c(c1)C(=O)c3c(n(nn3)c4cc(c(c(c4)F)c5cc(cc…
BCE Q02127 278.3 Da LogP 3.65 TPSA 73.1 ✓ Ro5 ✓ Clean CC(=C(C#N)C(=O)Nc1ccc(cc1)c2ccccc2)O
BRE Q02127 357.4 Da LogP 5.71 TPSA 50.2 1 viol. ✓ Clean Cc1c(c2cc(ccc2nc1c3ccc(cc3)c4ccccc4)F)C(=O)O
BVO Q02127 417.4 Da LogP 3.48 TPSA 85.1 ✓ Ro5 Alert c1ccc2c(c1)C(=O)c3c(n(nn3)c4cc(c(c(c4)F)c5cccc(…
CE9 Q02127 582.8 Da LogP 4.05 TPSA 103.3 1 viol. ✓ Clean CCCCCCCCCCCCOCCOCCOCCOCCOCCOCCOCCOCCOCCO
CHW Q02127 352.9 Da LogP 4.47 TPSA 77.8 ✓ Ro5 ✓ Clean Cc1c(c(c(c(c1Cl)O)C/C=C(\C)/CC/C=C(\C)/[C@H](C)…
CIH Q02127 347.2 Da LogP 4.95 TPSA 73.1 ✓ Ro5 ✓ Clean CC(=C(C#N)C(=O)Nc1ccc(c(c1)Cl)c2ccccc2Cl)O
CJH Q02127 322.4 Da LogP 4.05 TPSA 82.3 ✓ Ro5 ✓ Clean CCOc1cccc(c1)c2ccc(cc2)NC(=O)C(=C(C)O)C#N
DDQ Q02127 201.4 Da LogP 3.70 TPSA 23.1 ✓ Ro5 ✓ Clean CCCCCCCCCC[N+](C)(C)[O-]
DET Q02127 215.4 Da LogP 4.09 TPSA 23.1 ✓ Ro5 ✓ Clean CCCCCCCCCCC[N+](C)(C)[O-]
DOR Q02127 158.1 Da LogP -1.33 TPSA 95.5 ✓ Ro5 ✓ Clean C1[C@H](NC(=O)NC1=O)C(=O)O
DUH Q02127 401.3 Da LogP 4.52 TPSA 66.6 ✓ Ro5 ✓ Clean c1ccc(cc1)c2c(c(c(c(c2F)F)NC(=O)c3c4ccccn4nc3O)…
EZO Q02127 371.8 Da LogP 4.63 TPSA 65.8 ✓ Ro5 ✓ Clean CN(c1nc(cs1)c2ccccc2Cl)/N=C/c3ccccc3C(=O)O
F1W Q02127 454.6 Da LogP 4.78 TPSA 73.5 ✓ Ro5 ✓ Clean CC(C)(C)c1ccc(cc1)C(=O)NC(=S)Nc2ccc(cc2)NC(=O)C…
FNR Q02127 458.4 Da LogP -0.93 TPSA 208.4 1 viol. ✓ Clean Cc1cc2c(cc1C)N(C3=C(N2)C(=O)NC(=O)N3)C[C@@H]([C…
HYT Q02127 366.3 Da LogP 3.00 TPSA 80.0 ✓ Ro5 ✓ Clean Cn1nc(c(n1)O)C(=O)Nc2c(c(c(c(c2F)F)c3ccccc3)F)F
ILC Q02127 371.4 Da LogP 4.51 TPSA 75.6 ✓ Ro5 ✓ Clean COc1cccc(c1)c2ccc(c(c2)F)NC(=O)c3ccsc3C(=O)O
ILF Q02127 443.3 Da LogP 5.54 TPSA 75.6 1 viol. ✓ Clean c1cc(cc(c1)OC(F)(F)F)c2cc(c(c(c2)F)NC(=O)c3ccsc…
ILH Q02127 461.3 Da LogP 5.09 TPSA 75.6 1 viol. ✓ Clean c1cc(cc(c1)OC(F)(F)F)c2c(c(c(c(c2F)F)NC(=O)C3=C…
JJE Q02127 520.8 Da LogP 4.06 TPSA 98.4 1 viol. ✓ Clean CCN1C(=NN(C1=O)c2cc(c(cc2F)C(=O)Nc3c(cccc3Cl)F)…
JS3 Q02127 302.8 Da LogP 4.51 TPSA 42.0 ✓ Ro5 ✓ Clean Cc1c(sc(n1)Cl)C(=O)Nc2ccc3ccccc3c2
JTS Q02127 268.3 Da LogP 3.86 TPSA 42.0 ✓ Ro5 ✓ Clean Cc1c(scn1)C(=O)Nc2ccc3ccccc3c2
JTT Q02127 282.4 Da LogP 4.17 TPSA 42.0 ✓ Ro5 ✓ Clean Cc1c(sc(n1)C)C(=O)Nc2ccc3ccccc3c2
JTU Q02127 398.3 Da LogP 6.18 TPSA 50.2 1 viol. ✓ Clean CC[C@@H](C)c1ccc(cc1)c2c(c(c3cc(ccc3n2)Br)C(=O)…
KFZ Q02127 355.3 Da LogP 3.99 TPSA 63.3 ✓ Ro5 ✓ Clean CCc1cc(n2c(n1)nc(n2)SCc3cc(ccc3Cl)Cl)O
LDA Q02127 229.4 Da LogP 4.48 TPSA 23.1 ✓ Ro5 ✓ Clean CCCCCCCCCCCC[N+](C)(C)[O-]
M4J Q02127 460.5 Da LogP 5.76 TPSA 72.9 1 viol. ✓ Clean c1ccc2c(c1)ccc3c2ccc(c3)c4cc(nn4c5ccc(cc5)NC(=O…
MD7 Q02127 304.3 Da LogP 4.04 TPSA 73.1 ✓ Ro5 ✓ Clean c1ccc(cc1)c2ccc(cc2)NC(=O)C(=C(C3CC3)O)C#N
MDY Q02127 342.8 Da LogP 4.31 TPSA 82.4 ✓ Ro5 ✓ Clean CC(=C(C#N)C(=O)Nc1ccc(cc1Cl)c2ccccc2OC)O
ORO Q63707 156.1 Da LogP -1.24 TPSA 103.0 ✓ Ro5 ✓ Clean C1=C(NC(=O)NC1=O)C(=O)O
R2C Q02127 335.4 Da LogP 4.93 TPSA 67.8 ✓ Ro5 Alert COc1ccc(c(c1)C(=O)O)Nc2ccc(cc2)Oc3ccccc3
R4P Q02127 343.4 Da LogP 4.31 TPSA 68.0 ✓ Ro5 ✓ Clean Cc1ccccc1c2ccc(cc2)c3cc(c4c(c3)nnn4C)C(=O)O
SDV Q02127 376.4 Da LogP 3.96 TPSA 73.0 ✓ Ro5 ✓ Clean c1ccc2c(c1)c(on2)C(=O)N[C@@H]3CCCc4c3cnn4c5cccc…
U91 Q02127 379.3 Da LogP 3.91 TPSA 67.1 ✓ Ro5 ✓ Clean Cc1c(c(nn1C)O)C(=O)Nc2c(c(c(c(c2F)F)c3ccccc3)F)F
VGN Q02127 331.4 Da LogP 4.68 TPSA 66.4 ✓ Ro5 ✓ Clean CC(=O)Nc1ccc(cc1C(=O)O)c2ccc(cc2)c3ccccc3
VU7 Q02127 404.4 Da LogP 5.45 TPSA 51.2 1 viol. ✓ Clean Cc1c(c2cc(ccc2nc1c3ccc(cc3)c4ccccc4F)F)C(=O)NOC
W7A Q02127 336.3 Da LogP 2.21 TPSA 103.0 ✓ Ro5 ✓ Clean c1ccc(cc1)c2ccc(cc2)CCC3=C(NC(=O)NC3=O)C(=O)O
Y9B Q02127 369.3 Da LogP 3.72 TPSA 75.1 ✓ Ro5 ✓ Clean c1ccc(cc1)c2c(c(c(c(c2F)F)NC(=O)c3c(nsn3)O)F)F
ZWI Q02127 307.5 Da LogP 3.14 TPSA 57.2 ✓ Ro5 ✓ Clean CCCCCCCCCC[N+](C)(C)CCCS(=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.