Protein profile

PA2014

methylcrotonyl-CoA carboxylase subunit beta

Genome: NC_002516.2

Gene: liuB PA2014 Structure source: Experimental + AlphaFold UniProt Q9I297

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Amino acids 535

Annotations 5

Features 16

PDB binders 4

Druggability 0.857

Overview

Basic information about this protein and its source genome.

Accession: PA2014
Assembly: Pseudomonas aeruginosa PAO1, complete genome
Gene: liuB PA2014
Status: annotated
Amino acids: 535
Structure source: Experimental + AlphaFold

GO:1905202 A protein complex capable of methylcrotonoyl-CoA carboxylase activity. In mammals, it is a mitochondrial complex comprising a dodecamer of 6 alpha and 6 beta subunits: MCCC-alpha has a covalently bound biotin essential for the ATP-dependent carboxylation; MCCC-beta possesses carboxyltransferase activity which presumably is essential for binding to 3-methylcrotonyl-CoA. GO:0004485 Catalysis of the reaction: 3-methylbut-2-enoyl-CoA + ATP + bicarbonate = trans-3-methylglutaconyl-CoA + ADP + 2 H+ + phosphate. GO:0008300 The chemical reactions and pathways resulting in the breakdown of an isoprenoid compound, isoprene (2-methylbuta-1,3-diene) or compounds containing or derived from linked isoprene (3-methyl-2-butenylene) residues. GO:0006552 The chemical reactions and pathways resulting in the breakdown of L-leucine. GO:0016874 Catalysis of the joining of two molecules, or two groups within a single molecule, using the energy from the hydrolysis of ATP, a similar triphosphate, or a pH gradient.

Target profile

Computed evidence for target prioritization.

Human off-target: hit
Human identity (%): 68.519
Human E-value: 0.0
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 0.857

Structure –

Pocket –

Sequence

Primary amino-acid sequence viewer.

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

5 GO

Gene Ontology (GO)

GO:1905202 A protein complex capable of methylcrotonoyl-CoA carboxylase activity. In mammals, it is a mitochondrial complex comprising a dodecamer of 6 alpha and 6 beta subunits: MCCC-alpha has a covalently bound biotin essential for the ATP-dependent carboxylation; MCCC-beta possesses carboxyltransferase activity which presumably is essential for binding to 3-methylcrotonyl-CoA.
GO:0004485 Catalysis of the reaction: 3-methylbut-2-enoyl-CoA + ATP + bicarbonate = trans-3-methylglutaconyl-CoA + ADP + 2 H+ + phosphate.
GO:0008300 The chemical reactions and pathways resulting in the breakdown of an isoprenoid compound, isoprene (2-methylbuta-1,3-diene) or compounds containing or derived from linked isoprene (3-methyl-2-butenylene) residues.
GO:0006552 The chemical reactions and pathways resulting in the breakdown of L-leucine.
GO:0016874 Catalysis of the joining of two molecules, or two groups within a single molecule, using the energy from the hydrolysis of ATP, a similar triphosphate, or a pH gradient.

Sequence Features

Domain/signature hits from InterPro and related databases.

16 records

Show feature table

Start	End	DB	Term	Name
281	527	ProSiteProfiles	PS50989	Acetyl-coenzyme A (CoA) carboxyltransferase C-terminal domain profile.
281	527	InterPro	IPR011763	Acetyl-coenzyme A carboxyltransferase, C-terminal
2	535	PANTHER	PTHR22855	ACETYL, PROPIONYL, PYRUVATE, AND GLUTACONYL CARBOXYLASE-RELATED
2	535	InterPro	IPR045190	Methylcrotonoyl-CoA carboxylase beta chain MCCB/AccD1-like
23	270	SUPERFAMILY	SSF52096	ClpP/crotonase
23	270	InterPro	IPR029045	ClpP/crotonase-like domain superfamily
1	272	Gene3D	G3DSA:3.90.226.10	-
273	535	Gene3D	G3DSA:3.90.226.10	-
237	517	SUPERFAMILY	SSF52096	ClpP/crotonase
237	517	InterPro	IPR029045	ClpP/crotonase-like domain superfamily
2	272	FunFam	G3DSA:3.90.226.10:FF:000007	Methylcrotonoyl-CoA carboxylase subunit beta
274	535	FunFam	G3DSA:3.90.226.10:FF:000004	Methylcrotonoyl-CoA carboxylase beta chain
48	525	Pfam	PF01039	Carboxyl transferase domain
48	525	InterPro	IPR034733	Acetyl-CoA carboxylase
22	278	ProSiteProfiles	PS50980	Acetyl-coenzyme A (CoA) carboxyltransferase N-terminal domain profile.
22	278	InterPro	IPR011762	Acetyl-coenzyme A carboxyltransferase, N-terminal

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

3 + 1

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

Entry	Method	Resolution	Chain	Coverage	Links	Status
PDB 3U9R	X-ray	1.50 Å	B	100.0% 1-535	PDBe RCSB PDBj File	Viewing
PDB 3U9T	X-ray	2.90 Å	B	100.0% 1-535	PDBe RCSB PDBj File	Loaded
PDB 3U9S	X-ray	3.50 Å	B,D,F,H,J,L	100.0% 1-535	PDBe RCSB PDBj File	Loaded
AlphaFold PA2014	AlphaFold	—	—	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
3				0.752
9				0.385

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	16.19	0.773
2	6.78	0.346
3	5.82	0.284
4	4.18	0.17
5	2.87	0.09

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				0.49
1				0.318
13				0.203

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.

55 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.

Ligand	Source crystal	MW · LogP · TPSA	Lipinski	PAINS	SMILES
BTI	3U9S 3.50 Å Open crystal	228.3 Da LogP 0.91 TPSA 58.2	✓ Ro5	✓ Clean	`C1[C@H]2[C@@H]([C@@H](S1)CCCCC=O)NC(=O)N2`

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
1VU	1XNY	Q9X4K7	823.6 Da LogP -0.93 TPSA 363.6	3 viol.	✓ Clean	`CCC(=O)SCCNC(=O)CCNC(=O)[C@@H](C(C)(C)COP(=O)(O…`
DXX	1ON3	Q8GBW6	118.1 Da LogP -0.21 TPSA 74.6	✓ Ro5	✓ Clean	`CC(C(=O)O)C(=O)O`
MCA	1ON3	Q8GBW6	867.6 Da LogP -1.61 TPSA 400.9	3 viol.	✓ Clean	`C[C@H](C(=O)O)C(=O)SCCNC(=O)CCNC(=O)[C@@H](C(C)…`

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).

Ligand	UniProt (homolog)	pchembl	MW · LogP · TPSA	Lipinski	PAINS	SMILES
DWT	Q9HCC0	6.99	503.5 Da LogP 5.75 TPSA 97.6	2 viol.	✓ Clean	`Cc1ccc(cc1Nc2c3cn(nc3nc(n2)c4cccnc4)C)C(=O)Nc5c…`

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
ZINC34603442	0.703	215.3 Da LogP 0.28 TPSA 67.1	✓ Ro5	✓ Clean	`NCCCC[C@@H]1SC[C@@H]2NC(=O)N[C@H]12`
ZINC34182012	0.667	230.3 Da LogP 0.70 TPSA 61.4	✓ Ro5	✓ Clean	`O=C1N[C@@H]2[C@H](CCCCCO)SC[C@@H]2N1`
ZINC1532548	0.634	244.3 Da LogP 0.80 TPSA 78.4	✓ Ro5	✓ Clean	`O=C(O)CCCC[C@H]1SC[C@@H]2NC(=O)N[C@@H]21`
ZINC2169825	0.634	244.3 Da LogP 0.80 TPSA 78.4	✓ Ro5	✓ Clean	`O=C(O)CCCC[C@H]1SC[C@H]2NC(=O)N[C@H]21`
ZINC2169827	0.634	244.3 Da LogP 0.80 TPSA 78.4	✓ Ro5	✓ Clean	`O=C(O)CCCC[C@H]1SC[C@@H]2NC(=O)N[C@H]21`
ZINC3869709	0.634	243.3 Da LogP 0.20 TPSA 84.2	✓ Ro5	✓ Clean	`NC(=O)CCCC[C@@H]1SC[C@H]2NC(=O)N[C@@H]21`
ZINC3869710	0.634	243.3 Da LogP 0.20 TPSA 84.2	✓ Ro5	✓ Clean	`NC(=O)CCCC[C@@H]1SC[C@@H]2NC(=O)N[C@H]12`
ZINC3869711	0.634	243.3 Da LogP 0.20 TPSA 84.2	✓ Ro5	✓ Clean	`NC(=O)CCCC[C@@H]1SC[C@H]2NC(=O)N[C@H]21`
ZINC3869712	0.634	243.3 Da LogP 0.20 TPSA 84.2	✓ Ro5	✓ Clean	`NC(=O)CCCC[C@@H]1SC[C@@H]2NC(=O)N[C@@H]12`
ZINC22052067	0.609	301.4 Da LogP -0.09 TPSA 107.5	✓ Ro5	✓ Clean	`O=C(O)CNC(=O)CCCC[C@@H]1SC[C@@H]2NC(=O)N[C@H]12`
ZINC59286406	0.609	300.4 Da LogP -0.69 TPSA 113.3	✓ Ro5	✓ Clean	`NC(=O)CNC(=O)CCCC[C@@H]1SC[C@@H]2NC(=O)N[C@H]12`
ZINC222024244	0.600	283.4 Da LogP 0.99 TPSA 70.2	✓ Ro5	✓ Clean	`O=C(CCCC[C@@H]1SC[C@@H]2NC(=O)N[C@@H]12)NC1CC1`
ZINC48391181	0.600	283.4 Da LogP 0.99 TPSA 70.2	✓ Ro5	✓ Clean	`O=C(CCCC[C@@H]1SC[C@@H]2NC(=O)N[C@H]12)NC1CC1`
ZINC53464107	0.600	283.4 Da LogP 0.99 TPSA 70.2	✓ Ro5	✓ Clean	`O=C(CCCC[C@@H]1SC[C@H]2NC(=O)N[C@@H]21)NC1CC1`
ZINC53464111	0.600	283.4 Da LogP 0.99 TPSA 70.2	✓ Ro5	✓ Clean	`O=C(CCCC[C@@H]1SC[C@H]2NC(=O)N[C@H]21)NC1CC1`
ZINC2121285	0.578	258.3 Da LogP 0.89 TPSA 67.4	✓ Ro5	✓ Clean	`COC(=O)CCCC[C@@H]1SC[C@H]2NC(=O)N[C@H]21`
ZINC4038545	0.578	258.3 Da LogP 0.89 TPSA 67.4	✓ Ro5	✓ Clean	`COC(=O)CCCC[C@H]1SC[C@H]2NC(=O)N[C@H]21`
ZINC5005298	0.578	258.3 Da LogP 0.89 TPSA 67.4	✓ Ro5	✓ Clean	`COC(=O)CCCC[C@@H]1SC[C@H]2NC(=O)N[C@@H]21`
ZINC5224322	0.578	258.3 Da LogP 0.89 TPSA 67.4	✓ Ro5	✓ Clean	`COC(=O)CCCC[C@@H]1SC[C@@H]2NC(=O)N[C@H]12`
ZINC90514224	0.578	258.3 Da LogP 0.89 TPSA 67.4	✓ Ro5	✓ Clean	`COC(=O)CCCC[C@@H]1SC[C@@H]2NC(=O)N[C@@H]12`
ZINC27065097	0.574	311.5 Da LogP 1.77 TPSA 70.2	✓ Ro5	✓ Clean	`O=C(CCCC[C@@H]1SC[C@@H]2NC(=O)N[C@H]12)NC1CCCC1`
ZINC5157321	0.574	287.4 Da LogP -0.18 TPSA 90.5	✓ Ro5	✓ Clean	`O=C(CCCC[C@@H]1SC[C@@H]2NC(=O)N[C@H]12)NCCO`
ZINC206908803	0.571	315.4 Da LogP 0.00 TPSA 96.5	✓ Ro5	✓ Clean	`COC(=O)CNC(=O)CCCC[C@@H]1SC[C@H]2NC(=O)N[C@@H]21`
ZINC334161970	0.571	315.4 Da LogP 0.00 TPSA 96.5	✓ Ro5	✓ Clean	`COC(=O)CNC(=O)CCCC[C@@H]1SC[C@@H]2NC(=O)N[C@@H]…`
ZINC62001297	0.571	315.4 Da LogP 0.00 TPSA 96.5	✓ Ro5	✓ Clean	`COC(=O)CNC(=O)CCCC[C@@H]1SC[C@@H]2NC(=O)N[C@H]12`
ZINC75611263	0.571	315.4 Da LogP 0.00 TPSA 96.5	✓ Ro5	✓ Clean	`COC(=O)CNC(=O)CCCC[C@@H]1SC[C@H]2NC(=O)N[C@H]21`
ZINC104112886	0.568	242.3 Da LogP 0.57 TPSA 78.4	✓ Ro5	✓ Clean	`O=C(O)/C=C\CC[C@@H]1SC[C@H]2NC(=O)N[C@@H]21`
ZINC13543600	0.568	242.3 Da LogP 0.57 TPSA 78.4	✓ Ro5	✓ Clean	`O=C(O)/C=C\CC[C@@H]1SC[C@@H]2NC(=O)N[C@H]12`
ZINC4216800	0.568	242.3 Da LogP 0.57 TPSA 78.4	✓ Ro5	✓ Clean	`O=C(O)/C=C/CC[C@@H]1SC[C@@H]2NC(=O)N[C@H]12`
ZINC5082085	0.568	242.3 Da LogP 0.57 TPSA 78.4	✓ Ro5	✓ Clean	`O=C(O)/C=C/CC[C@@H]1SC[C@H]2NC(=O)N[C@@H]21`
ZINC5082088	0.568	242.3 Da LogP 0.57 TPSA 78.4	✓ Ro5	✓ Clean	`O=C(O)/C=C/CC[C@@H]1SC[C@H]2NC(=O)N[C@H]21`
ZINC5082090	0.568	242.3 Da LogP 0.57 TPSA 78.4	✓ Ro5	✓ Clean	`O=C(O)/C=C/CC[C@@H]1SC[C@@H]2NC(=O)N[C@@H]12`
ZINC77273222	0.568	428.6 Da LogP 1.36 TPSA 119.6	✓ Ro5	✓ Clean	`O=C1N[C@@H]2[C@H](CCCC(CCC[C@@H]3SC[C@@H]4NC(=O…`
ZINC107559942	0.563	283.4 Da LogP 1.01 TPSA 70.2	✓ Ro5	✓ Clean	`C=CCNC(=O)CCCC[C@@H]1SC[C@@H]2NC(=O)N[C@H]12`
ZINC12624504	0.563	339.5 Da LogP 2.55 TPSA 70.2	✓ Ro5	✓ Clean	`O=C(CCCC[C@@H]1SC[C@@H]2NC(=O)N[C@H]12)NC1CCCCC…`
ZINC13509480	0.563	315.4 Da LogP 0.30 TPSA 107.5	✓ Ro5	✓ Clean	`O=C(O)CCNC(=O)CCCC[C@@H]1SC[C@@H]2NC(=O)N[C@H]12`
ZINC141396702	0.563	303.5 Da LogP 0.76 TPSA 70.2	✓ Ro5	✓ Clean	`O=C(CCCC[C@@H]1SC[C@@H]2NC(=O)N[C@H]12)NCCS`
ZINC149421996	0.563	286.4 Da LogP -0.21 TPSA 96.2	✓ Ro5	✓ Clean	`NCCNC(=O)CCCC[C@H]1SC[C@H]2NC(=O)N[C@H]21`
ZINC22048411	0.563	286.4 Da LogP -0.21 TPSA 96.2	✓ Ro5	✓ Clean	`NCCNC(=O)CCCC[C@@H]1SC[C@H]2NC(=O)N[C@@H]21`
ZINC222218978	0.563	284.4 Da LogP 1.44 TPSA 67.4	✓ Ro5	✓ Clean	`C=CCOC(=O)CCCC[C@@H]1SC[C@@H]2NC(=O)N[C@@H]12`
ZINC222438745	0.563	339.5 Da LogP 2.55 TPSA 70.2	✓ Ro5	✓ Clean	`O=C(CCCC[C@@H]1SC[C@@H]2NC(=O)N[C@@H]12)NC1CCCC…`
ZINC34440530	0.563	301.4 Da LogP 0.21 TPSA 90.5	✓ Ro5	✓ Clean	`O=C(CCCC[C@@H]1SC[C@@H]2NC(=O)N[C@H]12)NCCCO`
ZINC39935771	0.563	286.4 Da LogP -0.21 TPSA 96.2	✓ Ro5	✓ Clean	`NCCNC(=O)CCCC[C@@H]1SC[C@H]2NC(=O)N[C@H]21`
ZINC39935772	0.563	286.4 Da LogP -0.21 TPSA 96.2	✓ Ro5	✓ Clean	`NCCNC(=O)CCCC[C@@H]1SC[C@@H]2NC(=O)N[C@@H]12`
ZINC5192432	0.563	286.4 Da LogP -0.21 TPSA 96.2	✓ Ro5	✓ Clean	`NCCNC(=O)CCCC[C@@H]1SC[C@@H]2NC(=O)N[C@H]12`
ZINC80301665	0.563	284.4 Da LogP 1.44 TPSA 67.4	✓ Ro5	✓ Clean	`C=CCOC(=O)CCCC[C@@H]1SC[C@@H]2NC(=O)N[C@H]12`
ZINC95966269	0.563	284.4 Da LogP 1.44 TPSA 67.4	✓ Ro5	✓ Clean	`C=CCOC(=O)CCCC[C@@H]1SC[C@H]2NC(=O)N[C@@H]21`
ZINC95966271	0.563	284.4 Da LogP 1.44 TPSA 67.4	✓ Ro5	✓ Clean	`C=CCOC(=O)CCCC[C@@H]1SC[C@H]2NC(=O)N[C@H]21`
ZINC9691512	0.563	339.5 Da LogP 2.55 TPSA 70.2	✓ Ro5	✓ Clean	`O=C(CCCC[C@@H]1SC[C@H]2NC(=O)N[C@@H]21)NC1CCCCC…`
ZINC9691514	0.563	339.5 Da LogP 2.55 TPSA 70.2	✓ Ro5	✓ Clean	`O=C(CCCC[C@@H]1SC[C@H]2NC(=O)N[C@H]21)NC1CCCCCC1`

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.