Protein profile

KP13_03277

2-oxoglutarate dehydrogenase E1 component

Genome: KpKP13

Gene: AHE45656.1 sucA Structure source: AlphaFold + ColabFold UniProt A0A0H3GQ15

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Amino acids 935

Annotations 7

Features 31

PDB binders 10

Druggability 0.729

Overview

Basic information about this protein and its source genome.

Accession: KP13_03277
Assembly: Klebsiella pneumoniae subsp. pneumoniae Kp13, complete sequence
Gene: AHE45656.1 sucA
Status: annotated
Amino acids: 935
Structure source: AlphaFold + ColabFold

1.2.4.2

GO:0016624 Catalysis of an oxidation-reduction (redox) reaction in which an aldehyde or ketone (oxo) group acts as a hydrogen or electron donor and reduces a disulfide. GO:0004591 Catalysis of the reaction: N(6)-[(R)-lipoyl]-L-lysyl-[dihydrolipoyllysine-residue succinyltransferase] + 2-oxoglutarate + H+ = N(6)-[(R)-S(8)-succinyldihydrolipoyl]-L-lysyl-[dihydrolipoyllysine-residue succinyltransferase] + CO2. GO:0030976 Binding to thiamine pyrophosphate, the diphosphoric ester of thiamine. Acts as a coenzyme of several (de)carboxylases, transketolases, and alpha-oxoacid dehydrogenases. 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:0005829 The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes. GO:0045252 A multi-enzyme complex that catalyzes the oxidative decarboxylation of alpha-ketoglutarate (also known as 2-oxoglutarate) to form succinyl-CoA. The complex comprises multiple copies of three enzymes referred to as E1, E2 and E3: oxoglutarate dehydrogenase (lipoamide) (E1), dihydrolipoamide S-succinyltransferase (E2) and dihydrolipoamide dehydrogenase (E3). Additional proteins may also be present.

Target profile

Computed evidence for target prioritization.

Human off-target: hit
Human identity (%): 47.101
Human E-value: 1.94e-39
Gut microbiome off-target: hit
Essential (DEG): Y
DEG identity (%): 93.797
DEG E-value: 0.0
Localization: Cytoplasmic
ColabFold pLDDT: 93.66

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 0.729

Structure A0A0H3GQ15

Pocket Pocket 49

P2Rank 0.835

Structure A0A0H3GQ15

Pocket Pocket 1

ColabFold model

FPocket 0.606 · Pocket 59

P2Rank 0.876 · Pocket 1

Core conservation Conserved core gene

Roary core

CoreCruncher core

Gut microbiome 195 / 4744 genomes with a hit

Normalized 0.041

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)

1.2.4.2

Gene Ontology (GO)

GO:0016624 Catalysis of an oxidation-reduction (redox) reaction in which an aldehyde or ketone (oxo) group acts as a hydrogen or electron donor and reduces a disulfide.
GO:0004591 Catalysis of the reaction: N(6)-[(R)-lipoyl]-L-lysyl-[dihydrolipoyllysine-residue succinyltransferase] + 2-oxoglutarate + H+ = N(6)-[(R)-S(8)-succinyldihydrolipoyl]-L-lysyl-[dihydrolipoyllysine-residue succinyltransferase] + CO2.
GO:0030976 Binding to thiamine pyrophosphate, the diphosphoric ester of thiamine. Acts as a coenzyme of several (de)carboxylases, transketolases, and alpha-oxoacid dehydrogenases.
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:0005829 The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
GO:0045252 A multi-enzyme complex that catalyzes the oxidative decarboxylation of alpha-ketoglutarate (also known as 2-oxoglutarate) to form succinyl-CoA. The complex comprises multiple copies of three enzymes referred to as E1, E2 and E3: oxoglutarate dehydrogenase (lipoamide) (E1), dihydrolipoamide S-succinyltransferase (E2) and dihydrolipoamide dehydrogenase (E3). Additional proteins may also be present.

Sequence Features

Domain/signature hits from InterPro and related databases.

31 records

Show feature table

Start	End	DB	Term	Name
593	787	Pfam	PF02779	Transketolase, pyrimidine binding domain
593	787	InterPro	IPR005475	Transketolase-like, pyrimidine-binding domain
12	50	Pfam	PF16078	2-oxoglutarate dehydrogenase N-terminus
12	50	InterPro	IPR032106	2-oxoglutarate dehydrogenase E1 component, N-terminal domain
1	934	PIRSF	PIRSF000157	Oxoglu_dh_E1
1	934	InterPro	IPR011603	2-oxoglutarate dehydrogenase E1 component
84	166	Gene3D	G3DSA:1.10.287.1150	TPP helical domain
576	793	SUPERFAMILY	SSF52518	Thiamin diphosphate-binding fold (THDP-binding)
576	793	InterPro	IPR029061	Thiamin diphosphate-binding fold
215	476	CDD	cd02016	TPP_E1_OGDC_like
828	848	Coils	Coil	Coil
790	932	Pfam	PF16870	2-oxoglutarate dehydrogenase C-terminal
790	932	InterPro	IPR031717	Multifunctional 2-oxoglutarate metabolism enzyme, C-terminal
14	932	NCBIfam	TIGR00239	2-oxoglutarate dehydrogenase E1 component
14	932	InterPro	IPR011603	2-oxoglutarate dehydrogenase E1 component
555	802	Gene3D	G3DSA:3.40.50.12470	-
791	931	FunFam	G3DSA:3.40.50.11610:FF:000001	2-oxoglutarate dehydrogenase E1 component
167	533	FunFam	G3DSA:3.40.50.970:FF:000014	2-oxoglutarate dehydrogenase E1 component
167	533	Gene3D	G3DSA:3.40.50.970	-
12	932	PANTHER	PTHR23152	2-OXOGLUTARATE DEHYDROGENASE
12	932	InterPro	IPR011603	2-oxoglutarate dehydrogenase E1 component
723	931	Gene3D	G3DSA:3.40.50.11610	-
723	931	InterPro	IPR042179	Multifunctional 2-oxoglutarate metabolism enzyme, C-terminal domain superfamily
221	506	Pfam	PF00676	Dehydrogenase E1 component
221	506	InterPro	IPR001017	Dehydrogenase, E1 component
593	786	SMART	SM00861	Transket_pyr_3
593	786	InterPro	IPR005475	Transketolase-like, pyrimidine-binding domain
84	166	FunFam	G3DSA:1.10.287.1150:FF:000004	2-oxoglutarate dehydrogenase E1 component
555	726	FunFam	G3DSA:3.40.50.12470:FF:000002	2-oxoglutarate dehydrogenase E1 component
120	548	SUPERFAMILY	SSF52518	Thiamin diphosphate-binding fold (THDP-binding)
120	548	InterPro	IPR029061	Thiamin diphosphate-binding fold

3D Structure

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

Loading 3D structure...

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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_A0A0H3GQ15	AlphaFold	—	—	full sequence	—	Viewing
ColabFold KP13_03277	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
49				0.729
50				0.673

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	Score	Probability
1	13.41	0.685
2	11.01	0.59
3	6.44	0.325
4	4.72	0.207
5	3.87	0.151

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
59				0.606
42				0.535
14				0.517
58				0.493

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	Score	Probability
1	14.67	0.73
2	12.5	0.653
3	4.41	0.186
4	3.44	0.124
5	3.34	0.118

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.

60 records

Highest-confidence structural evidence: ligands co-crystallized with this exact protein. If the source PDB is loaded in TPW, use Open crystal to inspect it in the structure viewer.

No PDB structure with a co-crystallized ligand found for this exact protein.

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.

Ligand	Source crystal	UniProt (homolog)	MW · LogP · TPSA	Lipinski	PAINS	SMILES
DW3	6KMA	A0A3Q0L1E1	60.1 Da LogP -0.82 TPSA 37.3	✓ Ro5	✓ Clean	`C(C=O)O`
JQ5	6R2C	A0R2B1	210.1 Da LogP 0.60 TPSA 100.9	✓ Ro5	✓ Clean	`CCOP(=O)(C(=O)CCC(=O)O)O`
OAA	6VEF	P0AFG3	131.1 Da LogP -2.22 TPSA 94.5	✓ Ro5	✓ Clean	`C(C(=O)C(=O)O)C(=O)[O-]`
QSP	6R29	A0R2B1	608.4 Da LogP 0.82 TPSA 283.4	3 viol.	✓ Clean	`Cc1ncc(c(n1)N)CN2[C@H](SC(=C2C)CCOP(=O)(O)OP(=O…`
TD6	3ZHS	A0R2B1	527.4 Da LogP 0.74 TPSA 226.5	2 viol.	✓ Clean	`Cc1c(sc([n+]1Cc2cnc(nc2N)C)[C@H](CCC(=O)O)O)CCO…`
TD7	2Y0P	A0R2B1	526.4 Da LogP 2.36 TPSA 225.9	3 viol.	✓ Clean	`Cc1ncc(c(n1)N)CN2C(=C(SC2=C(CCC(=O)O)O)CCO[P@](…`
TD8	3ZHU	A0R2B1	541.4 Da LogP 1.13 TPSA 226.5	2 viol.	✓ Clean	`Cc1c(sc([n+]1Cc2cnc(nc2N)C)[C@@H](CCCC(=O)O)O)C…`
TD9	3ZHT	A0R2B1	541.4 Da LogP 1.13 TPSA 226.5	2 viol.	✓ Clean	`Cc1c(sc([n+]1Cc2cnc(nc2N)C)[C@H](CCCC(=O)O)O)CC…`
TDW	3ZHV	A0R2B1	469.4 Da LogP 0.90 TPSA 189.2	✓ Ro5	✓ Clean	`Cc1c(sc([n+]1Cc2cnc(nc2N)C)[C@H](C)O)CCOP(=O)(O…`
ZP1	6R2A	A0R2B1	636.5 Da LogP 1.87 TPSA 272.4	3 viol.	✓ Clean	`CCOP(=O)([C@@](CCC(=O)O)([C@@H]1N(C(=C(S1)CCOP(…`

Experimental bioactivity from ChEMBL measured directly on this protein. Score = pchembl (−log Ki/IC₅₀; higher = more potent).

No ChEMBL bioactivity data found for this exact protein.

Bioactivity inferred from similar proteins in ChEMBL. Score = pchembl (−log Ki/IC₅₀; higher = more potent).

No ChEMBL hits found through similar proteins.

Proposed virtual-screening candidates from ZINC. Score = Tanimoto similarity to a known binder (0–1; higher = more similar).

Ligand	Tanimoto	MW · LogP · TPSA	Lipinski	PAINS	SMILES
ZINC12501520	1.000	458.5 Da LogP -0.88 TPSA 123.5	1 viol.	✓ Clean	`OCCOCCOCCOCCOCCOCCOCCOCCOCCOCCO`
ZINC3874716	1.000	414.5 Da LogP -0.90 TPSA 114.3	✓ Ro5	✓ Clean	`OCCOCCOCCOCCOCCOCCOCCOCCOCCO`
ZINC4283769	1.000	238.3 Da LogP -0.96 TPSA 77.4	✓ Ro5	✓ Clean	`OCCOCCOCCOCCOCCO`
ZINC4521548	1.000	282.3 Da LogP -0.95 TPSA 86.6	✓ Ro5	✓ Clean	`OCCOCCOCCOCCOCCOCCO`
ZINC5178829	1.000	326.4 Da LogP -0.93 TPSA 95.8	✓ Ro5	✓ Clean	`OCCOCCOCCOCCOCCOCCOCCO`
ZINC5178830	1.000	370.4 Da LogP -0.91 TPSA 105.1	✓ Ro5	✓ Clean	`OCCOCCOCCOCCOCCOCCOCCOCCO`
ZINC115086873	0.688	209.2 Da LogP -1.08 TPSA 83.2	✓ Ro5	✓ Clean	`NOCCOCCOCCOCCO`
ZINC137432264	0.688	457.6 Da LogP -0.91 TPSA 129.3	1 viol.	✓ Clean	`NCCOCCOCCOCCOCCOCCOCCOCCOCCOCCO`
ZINC146143823	0.688	237.3 Da LogP -1.00 TPSA 83.2	✓ Ro5	✓ Clean	`NCCOCCOCCOCCOCCO`
ZINC1542984442	0.688	413.5 Da LogP -0.93 TPSA 120.1	✓ Ro5	✓ Clean	`NCCOCCOCCOCCOCCOCCOCCOCCOCCO`
ZINC1565503710	0.688	254.3 Da LogP -0.03 TPSA 57.2	✓ Ro5	✓ Clean	`OCCOCCOCCOCCOCCS`
ZINC1580161	0.688	208.3 Da LogP -0.33 TPSA 57.2	✓ Ro5	✓ Clean	`COCCOCCOCCOCCO`
ZINC16052118	0.688	340.4 Da LogP -0.28 TPSA 84.8	✓ Ro5	✓ Clean	`COCCOCCOCCOCCOCCOCCOCCO`
ZINC16052257	0.688	384.5 Da LogP -0.26 TPSA 94.1	✓ Ro5	✓ Clean	`COCCOCCOCCOCCOCCOCCOCCOCCO`
ZINC1857792028	0.688	430.6 Da LogP 0.04 TPSA 94.1	✓ Ro5	✓ Clean	`OCCOCCOCCOCCOCCOCCOCCOCCOCCS`
ZINC1857792057	0.688	474.6 Da LogP 0.06 TPSA 103.3	1 viol.	✓ Clean	`OCCOCCOCCOCCOCCOCCOCCOCCOCCOCCS`
ZINC230494776	0.688	325.4 Da LogP -0.96 TPSA 101.6	✓ Ro5	✓ Clean	`NCCOCCOCCOCCOCCOCCOCCO`
ZINC34317654	0.688	472.6 Da LogP -0.23 TPSA 112.5	1 viol.	✓ Clean	`COCCOCCOCCOCCOCCOCCOCCOCCOCCOCCO`
ZINC38917157	0.688	210.3 Da LogP -0.04 TPSA 47.9	✓ Ro5	✓ Clean	`OCCOCCOCCOCCS`
ZINC44076059	0.688	428.5 Da LogP -0.24 TPSA 103.3	✓ Ro5	✓ Clean	`COCCOCCOCCOCCOCCOCCOCCOCCOCCO`
ZINC5210101	0.688	252.3 Da LogP -0.31 TPSA 66.4	✓ Ro5	✓ Clean	`COCCOCCOCCOCCOCCO`
ZINC5650743	0.688	222.3 Da LogP 0.07 TPSA 57.2	✓ Ro5	✓ Clean	`CCOCCOCCOCCOCCO`
ZINC5997860	0.688	296.4 Da LogP -0.29 TPSA 75.6	✓ Ro5	✓ Clean	`COCCOCCOCCOCCOCCOCCO`
ZINC6403917	0.688	354.4 Da LogP 0.11 TPSA 84.8	✓ Ro5	✓ Clean	`CCOCCOCCOCCOCCOCCOCCOCCO`
ZINC77271182	0.688	281.3 Da LogP -0.98 TPSA 92.4	✓ Ro5	✓ Clean	`NCCOCCOCCOCCOCCOCCO`
ZINC83253921	0.688	369.5 Da LogP -0.95 TPSA 110.9	✓ Ro5	✓ Clean	`NCCOCCOCCOCCOCCOCCOCCOCCO`
ZINC90741446	0.688	386.5 Da LogP 0.02 TPSA 84.8	✓ Ro5	✓ Clean	`OCCOCCOCCOCCOCCOCCOCCOCCS`
ZINC90741447	0.688	298.4 Da LogP -0.01 TPSA 66.4	✓ Ro5	✓ Clean	`OCCOCCOCCOCCOCCOCCS`
ZINC144169243	0.647	281.3 Da LogP -1.37 TPSA 89.4	✓ Ro5	✓ Clean	`OCCOCCOCCNCCOCCOCCO`
ZINC205758716	0.647	457.6 Da LogP -1.31 TPSA 126.3	1 viol.	✓ Clean	`OCCOCCOCCOCCOCCNCCOCCOCCOCCOCCO`
ZINC575441396	0.647	369.5 Da LogP -1.34 TPSA 107.9	✓ Ro5	✓ Clean	`OCCOCCOCCOCCNCCOCCOCCOCCO`
ZINC1644613	0.611	206.3 Da LogP 0.83 TPSA 47.9	✓ Ro5	✓ Clean	`CCCCOCCOCCOCCO`
ZINC258839852	0.611	276.3 Da LogP 0.61 TPSA 57.2	✓ Ro5	✓ Clean	`OCCOCCOCCOCCOCC(F)(F)F`
ZINC167715346	0.600	266.3 Da LogP -0.18 TPSA 77.4	✓ Ro5	✓ Clean	`OCCCOCCOCCOCCOCCCO`
ZINC34160867	0.600	222.3 Da LogP -0.20 TPSA 68.2	✓ Ro5	✓ Clean	`OCCCOCCOCCOCCCO`
ZINC8215517	0.592	425.3 Da LogP 0.84 TPSA 169.0	✓ Ro5	✓ Clean	`Cc1ncc(C[n+]2csc(CCO[P@@](=O)(O)OP(=O)(O)O)c2C)…`
ZINC1580159	0.588	210.3 Da LogP -0.26 TPSA 58.9	✓ Ro5	✓ Clean	`OCCOCCSCCOCCO`
ZINC1542984432	0.579	398.4 Da LogP -0.43 TPSA 122.1	✓ Ro5	✓ Clean	`O=C(O)CCOCCOCCOCCOCCOCCOCCOCCO`
ZINC207588231	0.579	207.3 Da LogP -0.75 TPSA 60.0	✓ Ro5	✓ Clean	`CNCCOCCOCCOCCO`
ZINC2555269	0.579	220.3 Da LogP 1.22 TPSA 47.9	✓ Ro5	✓ Clean	`CCCCCOCCOCCOCCO`
ZINC33967025	0.579	252.3 Da LogP -0.87 TPSA 94.5	✓ Ro5	✓ Clean	`O=C(O)COCCOCCOCCOCCO`
ZINC39267847	0.579	208.2 Da LogP -0.89 TPSA 85.2	✓ Ro5	✓ Clean	`O=C(O)COCCOCCOCCO`
ZINC575408819	0.579	383.5 Da LogP -1.00 TPSA 99.1	✓ Ro5	✓ Clean	`CN(CCOCCOCCOCCO)CCOCCOCCOCCO`
ZINC575440725	0.579	295.4 Da LogP -1.03 TPSA 80.6	✓ Ro5	✓ Clean	`CN(CCOCCOCCO)CCOCCOCCO`
ZINC83254085	0.579	354.4 Da LogP -0.45 TPSA 112.9	✓ Ro5	✓ Clean	`O=C(O)CCOCCOCCOCCOCCOCCOCCO`
ZINC83254087	0.579	266.3 Da LogP -0.48 TPSA 94.5	✓ Ro5	✓ Clean	`O=C(O)CCOCCOCCOCCOCCO`
ZINC95920522	0.579	296.3 Da LogP -0.85 TPSA 103.7	✓ Ro5	✓ Clean	`O=C(O)COCCOCCOCCOCCOCCO`
ZINC96503366	0.579	408.5 Da LogP -0.26 TPSA 94.1	✓ Ro5	✓ Clean	`C#CCOCCOCCOCCOCCOCCOCCOCCOCCO`
ZINC96503406	0.579	276.3 Da LogP -0.31 TPSA 66.4	✓ Ro5	✓ Clean	`C#CCOCCOCCOCCOCCOCCO`
ZINC96503526	0.579	442.5 Da LogP -0.41 TPSA 131.4	✓ Ro5	✓ Clean	`O=C(O)CCOCCOCCOCCOCCOCCOCCOCCOCCO`

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.