Protein profile

KP13_02900

Dihydrolipoamide acetyltransferase

Genome: KpKP13

Gene: AHE46176.1 Structure source: AlphaFold + ColabFold UniProt A0A0H3GSC6

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Amino acids 511

Annotations 4

Features 36

PDB binders 5

Druggability 0.894

Overview

Basic information about this protein and its source genome.

Accession: KP13_02900
Assembly: Klebsiella pneumoniae subsp. pneumoniae Kp13, complete sequence
Gene: AHE46176.1
Status: annotated
Amino acids: 511
Structure source: AlphaFold + ColabFold

2.3.1.-

GO:0045254 A multi-enzyme complex that catalyzes the oxidative decarboxylation of pyruvate to form acetyl-CoA. The complex comprises multiple copies of three enzymes referred to as E1, E2 and E3: pyruvate dehydrogenase (E1, which may be a homodimer or a heterotetramer of two alpha and two beta subunits, depending on species), dihydrolipoamide S-acetyltransferase (E2), and dihydrolipoamide dehydrogenase (E3). Additional proteins may also be present. GO:0016746 Catalysis of the transfer of an acyl group from one compound (donor) to another (acceptor). GO:0006086 The chemical reactions and pathways resulting in the formation of acetyl-CoA from pyruvate. In most organisms, this pathway links glycolysis to the TCA cycle, by a series of three reactions carried out by a multisubunit complex called the 'pyruvate dehydrogenase complex', even though pyruvate dehydrogenase activity describes only one of those reactions. The combination of the three reactions can be summarized as: pyruvate + coenzyme A + NAD+ -> acetyl-CoA + CO2 + NADH.

Target profile

Computed evidence for target prioritization.

Human off-target: hit
Human identity (%): 43.478
Human E-value: 9.17e-74
Gut microbiome off-target: hit
Essential (DEG): Y
DEG identity (%): 44.737
DEG E-value: 4.72e-77
Localization: Cytoplasmic
ColabFold pLDDT: 83.38

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 0.894

Structure A0A0H3GSC6

Pocket Pocket 22

P2Rank 0.37

Structure A0A0H3GSC6

Pocket Pocket 1

ColabFold model

FPocket 0.773 · Pocket 26

P2Rank 0.232 · Pocket 1

Core conservation Accessory gene

Roary accessory

CoreCruncher accessory

Gut microbiome 10 / 4744 genomes with a hit

Normalized 0.002

Sequence

Primary amino-acid sequence viewer.

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 3 GO

Enzyme Commission (EC)

2.3.1.-

Gene Ontology (GO)

GO:0045254 A multi-enzyme complex that catalyzes the oxidative decarboxylation of pyruvate to form acetyl-CoA. The complex comprises multiple copies of three enzymes referred to as E1, E2 and E3: pyruvate dehydrogenase (E1, which may be a homodimer or a heterotetramer of two alpha and two beta subunits, depending on species), dihydrolipoamide S-acetyltransferase (E2), and dihydrolipoamide dehydrogenase (E3). Additional proteins may also be present.
GO:0016746 Catalysis of the transfer of an acyl group from one compound (donor) to another (acceptor).
GO:0006086 The chemical reactions and pathways resulting in the formation of acetyl-CoA from pyruvate. In most organisms, this pathway links glycolysis to the TCA cycle, by a series of three reactions carried out by a multisubunit complex called the 'pyruvate dehydrogenase complex', even though pyruvate dehydrogenase activity describes only one of those reactions. The combination of the three reactions can be summarized as: pyruvate + coenzyme A + NAD+ -> acetyl-CoA + CO2 + NADH.

Sequence Features

Domain/signature hits from InterPro and related databases.

36 records

Show feature table

Start	End	DB	Term	Name
151	191	Gene3D	G3DSA:4.10.320.10	-
151	191	InterPro	IPR036625	E3-binding domain superfamily
218	258	Gene3D	G3DSA:4.10.320.10	-
218	258	InterPro	IPR036625	E3-binding domain superfamily
221	258	ProSiteProfiles	PS51826	Peripheral subunit-binding (PSBD) domain profile.
221	258	InterPro	IPR004167	Peripheral subunit-binding domain
214	257	SUPERFAMILY	SSF47005	Peripheral subunit-binding domain of 2-oxo acid dehydrogenase complex
214	257	InterPro	IPR036625	E3-binding domain superfamily
5	77	CDD	cd06849	lipoyl_domain
267	503	SUPERFAMILY	SSF52777	CoA-dependent acyltransferases
198	220	MobiDBLite	mobidb-lite	consensus disorder prediction
152	190	SUPERFAMILY	SSF47005	Peripheral subunit-binding domain of 2-oxo acid dehydrogenase complex
152	190	InterPro	IPR036625	E3-binding domain superfamily
29	58	ProSitePatterns	PS00189	2-oxo acid dehydrogenases acyltransferase component lipoyl binding site.
29	58	InterPro	IPR003016	2-oxo acid dehydrogenase, lipoyl-binding site
104	136	MobiDBLite	mobidb-lite	consensus disorder prediction
154	188	Pfam	PF02817	e3 binding domain
154	188	InterPro	IPR004167	Peripheral subunit-binding domain
221	255	Pfam	PF02817	e3 binding domain
221	255	InterPro	IPR004167	Peripheral subunit-binding domain
4	79	ProSiteProfiles	PS50968	Biotinyl/lipoyl domain profile.
4	79	InterPro	IPR000089	Biotin/lipoyl attachment
4	92	SUPERFAMILY	SSF51230	Single hybrid motif
4	92	InterPro	IPR011053	Single hybrid motif
266	504	FunFam	G3DSA:3.30.559.10:FF:000007	Dihydrolipoamide acetyltransferase component of pyruvate dehydrogenase complex
3	213	PANTHER	PTHR23151	DIHYDROLIPOAMIDE ACETYL/SUCCINYL-TRANSFERASE-RELATED
3	213	InterPro	IPR045257	Dihydrolipoamide acetyltransferase/Pyruvate dehydrogenase protein X component
278	503	Pfam	PF00198	2-oxoacid dehydrogenases acyltransferase (catalytic domain)
278	503	InterPro	IPR001078	2-oxoacid dehydrogenase acyltransferase, catalytic domain
6	76	Pfam	PF00364	Biotin-requiring enzyme
6	76	InterPro	IPR000089	Biotin/lipoyl attachment
261	507	Gene3D	G3DSA:3.30.559.10	-
261	507	InterPro	IPR023213	Chloramphenicol acetyltransferase-like domain superfamily
1	101	Gene3D	G3DSA:2.40.50.100	-
154	191	ProSiteProfiles	PS51826	Peripheral subunit-binding (PSBD) domain profile.
154	191	InterPro	IPR004167	Peripheral subunit-binding domain

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_A0A0H3GSC6	AlphaFold	—	—	full sequence	—	Viewing
ColabFold KP13_02900	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
22				0.894
31				0.356
12				0.348

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				3.37	0.12
2				3.23	0.112

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
26				0.773
29				0.239
1				0.238

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	2.95	0.095
2	2.63	0.076
3	2.03	0.045
4	1.33	0.015

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.

47 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
CAO	1EAC	P10802	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]([…`
DTT	1EAC	P10802	154.3 Da LogP -0.43 TPSA 40.5	✓ Ro5	✓ Clean	`C([C@@H]([C@H](CS)O)O)S`
LPM	1EAB	P10802	207.4 Da LogP 1.65 TPSA 43.1	✓ Ro5	✓ Clean	`C(CCC(=O)N)C[C@H](CCS)S`
RDC	2Q8I	P10515	364.8 Da LogP 2.69 TPSA 96.4	✓ Ro5	✓ Clean	`C[C@@H]1C[C@@H]2[C@H](O2)\C=C/C=C/C(=O)Cc3c(c(c…`
RED	1Y8N	P10515	208.3 Da LogP 2.25 TPSA 37.3	✓ Ro5	✓ Clean	`C(CCC(=O)O)C[C@H](CCS)S`

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
ZINC100006925	1.000	364.8 Da LogP 2.69 TPSA 96.4	✓ Ro5	✓ Clean	`C[C@@H]1C[C@H]2O[C@@H]2/C=C\C=C/C(=O)Cc2c(Cl)c(…`
ZINC100013319	1.000	364.8 Da LogP 2.69 TPSA 96.4	✓ Ro5	✓ Clean	`C[C@@H]1C[C@H]2O[C@H]2/C=C/C=C\C(=O)Cc2c(Cl)c(O…`
ZINC100013323	1.000	364.8 Da LogP 2.69 TPSA 96.4	✓ Ro5	✓ Clean	`C[C@H]1C[C@H]2O[C@H]2/C=C/C=C\C(=O)Cc2c(Cl)c(O)…`
ZINC100152234	1.000	364.8 Da LogP 2.69 TPSA 96.4	✓ Ro5	✓ Clean	`C[C@@H]1C[C@H]2O[C@@H]2/C=C/C=C/C(=O)Cc2c(Cl)c(…`
ZINC13521629	1.000	364.8 Da LogP 2.69 TPSA 96.4	✓ Ro5	✓ Clean	`C[C@@H]1C[C@H]2O[C@@H]2/C=C\C=C\C(=O)Cc2c(Cl)c(…`
ZINC2061000778	1.000	364.8 Da LogP 2.69 TPSA 96.4	✓ Ro5	✓ Clean	`C[C@H]1C[C@@H]2O[C@H]2C=CC=CC(=O)Cc2c(Cl)c(O)cc…`
ZINC253952046	1.000	364.8 Da LogP 2.69 TPSA 96.4	✓ Ro5	✓ Clean	`C[C@@H]1C[C@@H]2O[C@H]2C=CC=CC(=O)Cc2c(Cl)c(O)c…`
ZINC253987424	1.000	364.8 Da LogP 2.69 TPSA 96.4	✓ Ro5	✓ Clean	`C[C@@H]1C[C@H]2O[C@@H]2C=CC=CC(=O)Cc2c(Cl)c(O)c…`
ZINC253987427	1.000	364.8 Da LogP 2.69 TPSA 96.4	✓ Ro5	✓ Clean	`C[C@@H]1C[C@H]2O[C@H]2C=CC=CC(=O)Cc2c(Cl)c(O)cc…`
ZINC253987428	1.000	364.8 Da LogP 2.69 TPSA 96.4	✓ Ro5	✓ Clean	`C[C@@H]1C[C@@H]2O[C@@H]2C=CC=CC(=O)Cc2c(Cl)c(O)…`
ZINC33838895	1.000	364.8 Da LogP 2.69 TPSA 96.4	✓ Ro5	✓ Clean	`C[C@@H]1C[C@H]2O[C@H]2/C=C\C=C/C(=O)Cc2c(Cl)c(O…`
ZINC45789132	1.000	364.8 Da LogP 2.69 TPSA 96.4	✓ Ro5	✓ Clean	`C[C@@H]1C[C@H]2O[C@@H]2/C=C/C=C\C(=O)Cc2c(Cl)c(…`
ZINC45789135	1.000	364.8 Da LogP 2.69 TPSA 96.4	✓ Ro5	✓ Clean	`C[C@H]1C[C@H]2O[C@@H]2/C=C/C=C\C(=O)Cc2c(Cl)c(O…`
ZINC5492965	1.000	364.8 Da LogP 2.69 TPSA 96.4	✓ Ro5	✓ Clean	`C[C@@H]1C[C@@H]2O[C@H]2/C=C\C=C\C(=O)Cc2c(Cl)c(…`
ZINC1529363	0.704	208.3 Da LogP 2.25 TPSA 37.3	✓ Ro5	✓ Clean	`O=C(O)CCCC[C@H](S)CCS`
ZINC3869601	0.704	208.3 Da LogP 2.25 TPSA 37.3	✓ Ro5	✓ Clean	`O=C(O)CCCC[C@@H](S)CCS`
ZINC12501123	0.566	427.2 Da LogP -1.75 TPSA 232.6	2 viol.	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](COP(=O)(O)O)[C@@H](…`
ZINC4228234	0.566	427.2 Da LogP -1.75 TPSA 232.6	2 viol.	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](COP(=O)(O)O)[C@@H](…`
ZINC79671662	0.566	427.2 Da LogP -1.75 TPSA 232.6	2 viol.	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](COP(=O)(O)O)[C@H](O…`
ZINC79671663	0.566	427.2 Da LogP -1.75 TPSA 232.6	2 viol.	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](COP(=O)(O)O)[C@H](O…`
ZINC44630074	0.538	217.4 Da LogP 2.91 TPSA 43.1	✓ Ro5	✓ Clean	`NC(=O)CCCCCCCCCCS`
ZINC95910974	0.538	287.5 Da LogP 4.86 TPSA 43.1	✓ Ro5	✓ Clean	`NC(=O)CCCCCCCCCCCCCCCS`
ZINC12360002	0.523	427.2 Da LogP -1.75 TPSA 232.6	2 viol.	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](CO[P@@](=O)(O)OP(=O…`
ZINC12360703	0.523	427.2 Da LogP -1.75 TPSA 232.6	2 viol.	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](CO[P@@](=O)(O)OP(=O…`
ZINC12503599	0.523	427.2 Da LogP -1.75 TPSA 232.6	2 viol.	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](CO[P@@](=O)(O)OP(=O…`
ZINC16546165	0.523	427.2 Da LogP -1.75 TPSA 232.6	2 viol.	✓ Clean	`Nc1ncnc2c1ncn2[C@H]1O[C@H](CO[P@](=O)(O)OP(=O)(…`
ZINC31977053	0.523	427.2 Da LogP -1.75 TPSA 232.6	2 viol.	✓ Clean	`Nc1ncnc2c1ncn2[C@H]1O[C@@H](CO[P@](=O)(O)OP(=O)…`
ZINC4806433	0.523	427.2 Da LogP -1.75 TPSA 232.6	2 viol.	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](CO[P@@](=O)(O)OP(=O…`
ZINC53683898	0.523	427.2 Da LogP -1.75 TPSA 232.6	2 viol.	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@@H](CO[P@@](=O)(O)OP(=…`
ZINC8586019	0.523	427.2 Da LogP -1.75 TPSA 232.6	2 viol.	✓ Clean	`Nc1ncnc2c1ncn2[C@H]1O[C@@H](CO[P@](=O)(O)OP(=O)…`
ZINC8586020	0.523	427.2 Da LogP -1.75 TPSA 232.6	2 viol.	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@@H](CO[P@@](=O)(O)OP(=…`
ZINC8586021	0.523	427.2 Da LogP -1.75 TPSA 232.6	2 viol.	✓ Clean	`Nc1ncnc2c1ncn2[C@H]1O[C@@H](CO[P@@](=O)(O)OP(=O…`
ZINC8586022	0.523	427.2 Da LogP -1.75 TPSA 232.6	2 viol.	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@@H](CO[P@@](=O)(O)OP(=…`
ZINC3871401	0.517	427.2 Da LogP -1.75 TPSA 232.6	2 viol.	✓ Clean	`Nc1ncnc2c1ncn2[C@H]1O[C@@H](COP(=O)(O)O)[C@@H](…`
ZINC3871402	0.517	427.2 Da LogP -1.75 TPSA 232.6	2 viol.	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@@H](COP(=O)(O)O)[C@@H]…`
ZINC3871403	0.517	427.2 Da LogP -1.75 TPSA 232.6	2 viol.	✓ Clean	`Nc1ncnc2c1ncn2[C@H]1O[C@@H](COP(=O)(O)O)[C@@H](…`
ZINC3871404	0.517	427.2 Da LogP -1.75 TPSA 232.6	2 viol.	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@@H](COP(=O)(O)O)[C@@H]…`
ZINC4096223	0.517	427.2 Da LogP -1.75 TPSA 232.6	2 viol.	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](COP(=O)(O)O)[C@@H](…`
ZINC12958381	0.506	347.2 Da LogP -1.86 TPSA 186.1	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](CO)[C@@H](OP(=O)(O)…`
ZINC13546985	0.506	347.2 Da LogP -1.86 TPSA 186.1	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](CO)[C@H](OP(=O)(O)O…`
ZINC1631259	0.506	347.2 Da LogP -1.86 TPSA 186.1	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](CO)[C@@H](OP(=O)(O)…`
ZINC79090744	0.506	347.2 Da LogP -1.86 TPSA 186.1	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](CO)[C@H](OP(=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.