Protein profile

VK055_1793

succinyl-CoA synthetase, alpha subunit

Genome: KpATCC43816

Gene: sucD AIK80406.1 Structure source: AlphaFold + ColabFold UniProt A0A0H3GK43
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Amino acids 289
Annotations 7
Features 30
PDB binders 12
Druggability 0.867

Overview

Basic information about this protein and its source genome.

Accession
VK055_1793
Assembly
Klebsiella pneumoniae subsp. pneumoniae strain ATCC 43816 KPPR1, complete genome
Gene
sucD AIK80406.1
Status
annotated
Amino acids
289
Structure source
AlphaFold + ColabFold
EC
6.2.1.5
GO
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. 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: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: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.

Target profile

Computed evidence for target prioritization.

Human off-target
hit
Human identity (%)
68.707
Human E-value
5.6300000000000005e-64
Gut microbiome off-target
hit
Essential (DEG)
Y
DEG identity (%)
95.502
DEG E-value
0.0
Localization
Cytoplasmic
ColabFold pLDDT
97.53

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 0.867
Structure A0A0H3GK43
Pocket Pocket 2
P2Rank 0.102
Structure A0A0H3GK43
Pocket Pocket 1
ColabFold model
FPocket 0.545 · Pocket 3
P2Rank 0.11 · Pocket 1
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 579 / 4744 genomes with a hit
Normalized 0.122

Sequence

Primary amino-acid sequence viewer.

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 6 GO

Enzyme Commission (EC)

1

Gene Ontology (GO)

6
  • 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.
  • 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: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: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.

Sequence Features

Domain/signature hits from InterPro and related databases.

30 records
Show feature table
Start End DB Term Name
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
3 287 PANTHER PTHR11117 SUCCINYL-COA LIGASE SUBUNIT ALPHA
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
1 289 PIRSF PIRSF001553 SucCS_alpha
1 289 InterPro IPR005810 Succinyl-CoA ligase, alpha subunit
120 289 FunFam G3DSA:3.40.50.261:FF:000002 Succinate--CoA ligase [ADP-forming] subunit alpha
1 119 Gene3D G3DSA:3.40.50.720 -
123 287 SUPERFAMILY SSF52210 Succinyl-CoA synthetase domains
123 287 InterPro IPR016102 Succinyl-CoA synthetase-like
151 271 Pfam PF00549 CoA-ligase
151 271 InterPro IPR005811 ATP-citrate lyase/succinyl-CoA ligase
1 122 SUPERFAMILY SSF51735 NAD(P)-binding Rossmann-fold domains
1 122 InterPro IPR036291 NAD(P)-binding domain superfamily
1 120 FunFam G3DSA:3.40.50.720:FF:000002 Succinate--CoA ligase [ADP-forming] subunit alpha
120 289 Gene3D G3DSA:3.40.50.261 -
120 289 InterPro IPR016102 Succinyl-CoA synthetase-like
4 287 NCBIfam TIGR01019 succinate--CoA ligase subunit alpha
4 287 InterPro IPR005810 Succinyl-CoA ligase, alpha subunit
1 288 Hamap MF_01988 Succinate--CoA ligase [ADP-forming] subunit alpha [sucD].
1 288 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
6 99 Pfam PF02629 CoA binding domain
6 99 InterPro IPR003781 CoA-binding
4 100 SMART SM00881 CoA_binding_2
4 100 InterPro IPR003781 CoA-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 + 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_A0A0H3GK43
AlphaFold — — full sequence — Viewing
ColabFold VK055_1793
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
2 0.867

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 2.11 0.048
2 1.4 0.018
3 1.31 0.014

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
5TDM
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
5TDF
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
6HXL
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
6XRU
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
6HXK
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
6O0H
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
6UV5
P53396 131.1 Da LogP -2.22 TPSA 94.5 ✓ Ro5 ✓ Clean C(C(=O)C(=O)O)C(=O)[O-]
Q5B
6Z2H
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
5CAE
O19069 118.1 Da LogP -0.06 TPSA 74.6 ✓ Ro5 ✓ Clean C(CC(=O)O)C(=O)O
TLA
3PFF
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
6WCV
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
7LIW
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.