Protein profile

PA1589

succinyl-CoA ligase subunit alpha

Genome: NC_002516.2

Gene: PA1589 sucD Structure source: AlphaFold UniProt Q51567
Amino acids 295
Annotations 10
Features 30
PDB binders 12
Druggability 0.846

Overview

Basic information about this protein and its source genome.

Accession
PA1589
Gene
PA1589 sucD
Status
annotated
Amino acids
295
Structure source
AlphaFold

Target profile

Computed evidence for target prioritization.

Human off-target
hit
Human identity (%)
68.707
Human E-value
2.31e-63
Gut microbiome off-target
hit
Essential (DEG)
Y
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 0.846
Structure
Pocket

Sequence

Primary amino-acid sequence viewer.

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 9 GO

Enzyme Commission (EC)

1

Gene Ontology (GO)

9
  • GO:0042709 A heterodimeric enzyme complex, usually composed of an alpha and beta chain. Functions in the TCA cycle, hydrolyzing succinyl-CoA into succinate and CoA, thereby forming ATP or GTP.
  • GO:0009361 A heterodimeric enzyme complex, composed of an alpha and beta chain, most usually found in (but not limited to) bacteria. Functions in the TCA cycle, hydrolyzing succinyl-CoA into succinate and CoA, thereby forming ATP.
  • GO:0004550 Catalysis of the reaction: ATP + nucleoside diphosphate = ADP + nucleoside triphosphate.
  • GO:0000166 Binding to a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
  • GO:0004775 Catalysis of the reaction: ATP + succinate + CoA = ADP + succinyl-CoA + phosphate.
  • GO:0004776 Catalysis of the reaction: GTP + succinate + CoA = GDP + succinyl-CoA + phosphate.
  • GO:0009142 The chemical reactions and pathways resulting in the formation of a nucleoside triphosphate, a compound consisting of a nucleobase linked to a deoxyribose or ribose sugar esterified with triphosphate on the sugar.
  • GO:0006099 A nearly universal metabolic pathway in which the acetyl group of acetyl coenzyme A is effectively oxidized to two CO2 and four pairs of electrons are transferred to coenzymes. The acetyl group combines with oxaloacetate to form citrate, which undergoes successive transformations to isocitrate, 2-oxoglutarate, succinyl-CoA, succinate, fumarate, malate, and oxaloacetate again, thus completing the cycle. In eukaryotes the tricarboxylic acid is confined to the mitochondria. See also glyoxylate cycle.
  • GO:0003824 Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.

Sequence Features

Domain/signature hits from InterPro and related databases.

30 records
Show feature table
Start End DB Term Name
3 287 PANTHER PTHR11117 SUCCINYL-COA LIGASE SUBUNIT ALPHA
6 99 Pfam PF02629 CoA binding domain
6 99 InterPro IPR003781 CoA-binding
1 290 PIRSF PIRSF001553 SucCS_alpha
1 290 InterPro IPR005810 Succinyl-CoA ligase, alpha subunit
152 181 ProSitePatterns PS01216 ATP-citrate lyase / succinyl-CoA ligases family signature 1.
152 181 InterPro IPR033847 ATP-citrate lyase/succinyl-CoA ligase, conserved site
120 290 FunFam G3DSA:3.40.50.261:FF:000002 Succinate--CoA ligase [ADP-forming] subunit alpha
1 120 FunFam G3DSA:3.40.50.720:FF:000002 Succinate--CoA ligase [ADP-forming] subunit alpha
120 293 Gene3D G3DSA:3.40.50.261 -
120 293 InterPro IPR016102 Succinyl-CoA synthetase-like
151 270 Pfam PF00549 CoA-ligase
151 270 InterPro IPR005811 ATP-citrate lyase/succinyl-CoA ligase
1 288 Hamap MF_01988 Succinate--CoA ligase [ADP-forming] subunit alpha [sucD].
1 288 InterPro IPR005810 Succinyl-CoA ligase, alpha subunit
1 122 SUPERFAMILY SSF51735 NAD(P)-binding Rossmann-fold domains
1 122 InterPro IPR036291 NAD(P)-binding domain superfamily
123 289 SUPERFAMILY SSF52210 Succinyl-CoA synthetase domains
123 289 InterPro IPR016102 Succinyl-CoA synthetase-like
236 249 ProSitePatterns PS00399 ATP-citrate lyase / succinyl-CoA ligases family active site.
236 249 InterPro IPR017440 ATP-citrate lyase/succinyl-CoA ligase, active site
4 100 SMART SM00881 CoA_binding_2
4 100 InterPro IPR003781 CoA-binding
1 119 Gene3D G3DSA:3.40.50.720 -
82 99 PRINTS PR01798 Succinyl-CoA synthase signature
208 221 PRINTS PR01798 Succinyl-CoA synthase signature
240 257 PRINTS PR01798 Succinyl-CoA synthase signature
177 195 PRINTS PR01798 Succinyl-CoA synthase signature
4 287 NCBIfam TIGR01019 succinate--CoA ligase subunit alpha
4 287 InterPro IPR005810 Succinyl-CoA ligase, alpha subunit

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

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

Entry Method Resolution Chain Coverage Links Status
AlphaFold PA1589
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
5 0.846
4 0.241

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.

118 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
7A2 P53396 208.1 Da LogP -2.28 TPSA 152.4 ✓ Ro5 ✓ Clean C(C(=O)O)[C@]([C@H](C(=O)O)O)(C(=O)O)O
7A3 P53396 208.1 Da LogP -2.28 TPSA 152.4 ✓ Ro5 ✓ Clean C(C(=O)O)[C@]([C@@H](C(=O)O)O)(C(=O)O)O
CAO P53396 783.5 Da LogP -1.39 TPSA 366.8 3 viol. ✓ Clean CC(C)(CO[P@](=O)(O)O[P@](=O)(O)OC[C@@H]1[C@H]([…
DCA O19069 735.5 Da LogP -1.58 TPSA 346.6 3 viol. ✓ Clean CCNC(=O)CCNC(=O)[C@@H](C(C)(C)CO[P@@](=O)(O)O[P…
FLC P53396 189.1 Da LogP -5.25 TPSA 140.6 ✓ Ro5 ✓ Clean C(C(=O)[O-])C(CC(=O)[O-])(C(=O)[O-])O
LBG P53396 453.9 Da LogP 4.58 TPSA 92.7 ✓ Ro5 ✓ Clean COC(=O)c1cc(c(c(c1)Cl)O)S(=O)(=O)Nc2cc(c(cc2F)F…
OAA P53396 131.1 Da LogP -2.22 TPSA 94.5 ✓ Ro5 ✓ Clean C(C(=O)C(=O)O)C(=O)[O-]
Q5B P53396 941.6 Da LogP -2.65 TPSA 458.5 3 viol. ✓ Clean CC(C)(COP(=O)(O)OP(=O)(O)OC[C@@H]1[C@H]([C@H]([…
SIN O19069 118.1 Da LogP -0.06 TPSA 74.6 ✓ Ro5 ✓ Clean C(CC(=O)O)C(=O)O
TLA P53396 150.1 Da LogP -2.12 TPSA 115.1 ✓ Ro5 ✓ Clean [C@@H]([C@H](C(=O)O)O)(C(=O)O)O
TUY P53597 899.6 Da LogP -3.53 TPSA 441.4 3 viol. ✓ Clean CC(C)(COP(=O)(O)OP(=O)(O)OC[C@@H]1[C@H]([C@H]([…
Y2A P53396 272.1 Da LogP -1.70 TPSA 178.7 ✓ Ro5 ✓ Clean C(C(=O)O)[C@](CC(=O)OP(=O)(O)O)(C(=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.