Protein profile

PA4997

transporter MsbA

Genome: NC_002516.2

Gene: msbA PA4997 Structure source: AlphaFold UniProt Q9HUG8

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Amino acids 603

Annotations 12

Features 43

PDB binders 4

Druggability 0.91

Overview

Basic information about this protein and its source genome.

Accession: PA4997
Assembly: Pseudomonas aeruginosa PAO1, complete genome
Gene: msbA PA4997
Status: annotated
Amino acids: 603
Structure source: AlphaFold

7.5.2.6

GO:0005886 The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins. GO:0140359 Primary active transporter characterized by two nucleotide-binding domains and two transmembrane domains. Uses the energy generated from ATP hydrolysis to drive the transport of a substance across a membrane. GO:0005524 Binding to ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator. GO:0016887 Catalysis of the reaction: ATP + H2O = ADP + H+ phosphate. ATP hydrolysis is used in some reactions as an energy source, for example to catalyze a reaction or drive transport against a concentration gradient. GO:0005347 Enables the transfer of ATP, adenosine triphosphate, from one side of a membrane to the other. GO:0034040 Enables the transfer of a solute or solutes from one side of a membrane to the other according to the reaction: ATP + H2O + lipid(in) = ADP + phosphate + lipid(out).

Target profile

Computed evidence for target prioritization.

Human off-target: hit
Human identity (%): 58.442
Human E-value: 9.74e-23
Gut microbiome off-target: hit
Essential (DEG): Y
Localization: CytoplasmicMembrane

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 0.91

Structure –

Pocket –

Sequence

Primary amino-acid sequence viewer.

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 11 GO

Enzyme Commission (EC)

7.5.2.6

Gene Ontology (GO)

GO:0005886 The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.
GO:0140359 Primary active transporter characterized by two nucleotide-binding domains and two transmembrane domains. Uses the energy generated from ATP hydrolysis to drive the transport of a substance across a membrane.
GO:0005524 Binding to ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
GO:0016887 Catalysis of the reaction: ATP + H2O = ADP + H+ phosphate. ATP hydrolysis is used in some reactions as an energy source, for example to catalyze a reaction or drive transport against a concentration gradient.
GO:0005347 Enables the transfer of ATP, adenosine triphosphate, from one side of a membrane to the other.
GO:0034040 Enables the transfer of a solute or solutes from one side of a membrane to the other according to the reaction: ATP + H2O + lipid(in) = ADP + phosphate + lipid(out).
GO:0042626 Primary active transporter of a solute across a membrane, via the reaction: ATP + H2O = ADP + phosphate, to directly drive the transport of a substance across a membrane. The transport protein may be transiently phosphorylated (P-type transporters), or not (ABC-type transporters and other families of transporters). Primary active transport occurs up the solute's concentration gradient and is driven by a primary energy source.
GO:0009245 The chemical reactions and pathways resulting in the formation of lipid A, the glycolipid group of bacterial lipopolysaccharides, consisting of four to six fatty acyl chains linked to two glucosamine residues. Further modifications of the backbone are common.
GO:0015920 The directed movement of lipopolysaccharides into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. A lipopolysaccharide is any of a group of related, structurally complex components of the outer membrane of Gram-negative bacteria. Lipopolysaccharides consist three covalently linked regions, lipid A, core oligosaccharide, and an O side chain. Lipid A is responsible for the toxicity of the lipopolysaccharide.
GO:0055085 The process in which a solute is transported across a lipid bilayer, from one side of a membrane to the other.
GO:0016020 A lipid bilayer along with all the proteins and protein complexes embedded in it and attached to it.

Sequence Features

Domain/signature hits from InterPro and related databases.

43 records

Show feature table

Start	End	DB	Term	Name
6	342	Gene3D	G3DSA:1.20.1560.10	ABC transporter type 1, transmembrane domain
6	342	InterPro	IPR036640	ABC transporter type 1, transmembrane domain superfamily
347	596	FunFam	G3DSA:3.40.50.300:FF:000140	Lipid A export ATP-binding/permease protein MsbA
203	265	Phobius	CYTOPLASMIC_DOMAIN	Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
161	178	TMHMM	TMhelix	Region of a membrane-bound protein predicted to be embedded in the membrane.
343	593	Gene3D	G3DSA:3.40.50.300	-
343	593	InterPro	IPR027417	P-loop containing nucleoside triphosphate hydrolase
346	591	SUPERFAMILY	SSF52540	P-loop containing nucleoside triphosphate hydrolases
346	591	InterPro	IPR027417	P-loop containing nucleoside triphosphate hydrolase
15	595	NCBIfam	TIGR02203	lipid A export permease/ATP-binding protein MsbA
15	595	InterPro	IPR011917	ABC transporter, lipid A-core flippase, MsbA
266	289	Phobius	TRANSMEMBRANE	Region of a membrane-bound protein predicted to be embedded in the membrane.
79	101	TMHMM	TMhelix	Region of a membrane-bound protein predicted to be embedded in the membrane.
266	288	TMHMM	TMhelix	Region of a membrane-bound protein predicted to be embedded in the membrane.
106	160	Phobius	CYTOPLASMIC_DOMAIN	Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
20	42	TMHMM	TMhelix	Region of a membrane-bound protein predicted to be embedded in the membrane.
356	592	ProSiteProfiles	PS50893	ATP-binding cassette, ABC transporter-type domain profile.
356	592	InterPro	IPR003439	ABC transporter-like, ATP-binding domain
382	575	SMART	SM00382	AAA_5
382	575	InterPro	IPR003593	AAA+ ATPase domain
21	41	Phobius	TRANSMEMBRANE	Region of a membrane-bound protein predicted to be embedded in the membrane.
79	105	Phobius	TRANSMEMBRANE	Region of a membrane-bound protein predicted to be embedded in the membrane.
183	202	TMHMM	TMhelix	Region of a membrane-bound protein predicted to be embedded in the membrane.
495	509	ProSitePatterns	PS00211	ABC transporters family signature.
495	509	InterPro	IPR017871	ABC transporter-like, conserved site
161	178	Phobius	TRANSMEMBRANE	Region of a membrane-bound protein predicted to be embedded in the membrane.
30	332	CDD	cd18552	ABC_6TM_MsbA_like
373	523	Pfam	PF00005	ABC transporter
373	523	InterPro	IPR003439	ABC transporter-like, ATP-binding domain
18	338	SUPERFAMILY	SSF90123	ABC transporter transmembrane region
18	338	InterPro	IPR036640	ABC transporter type 1, transmembrane domain superfamily
356	590	CDD	cd03251	ABCC_MsbA
290	603	Phobius	NON_CYTOPLASMIC_DOMAIN	Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
184	202	Phobius	TRANSMEMBRANE	Region of a membrane-bound protein predicted to be embedded in the membrane.
42	78	Phobius	NON_CYTOPLASMIC_DOMAIN	Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
1	20	Phobius	CYTOPLASMIC_DOMAIN	Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
31	306	Pfam	PF00664	ABC transporter transmembrane region
31	306	InterPro	IPR011527	ABC transporter type 1, transmembrane domain
179	183	Phobius	NON_CYTOPLASMIC_DOMAIN	Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
85	589	PANTHER	PTHR24221	ATP-BINDING CASSETTE SUB-FAMILY B
85	589	InterPro	IPR039421	Type 1 protein exporter
31	324	ProSiteProfiles	PS50929	ABC transporter integral membrane type-1 fused domain profile.
31	324	InterPro	IPR011527	ABC transporter type 1, transmembrane domain

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 PA4997	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
14				0.67
8				0.654
23				0.437

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.

54 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
AGS	6QUZ	Q9WYC4	523.2 Da LogP -1.51 TPSA 262.1	3 viol.	✓ Clean	`c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)…`
ANP	3B60	P63359	506.2 Da LogP -2.06 TPSA 281.9	3 viol.	✓ Clean	`c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)…`
Y01	5OCH	Q9NUT2	486.7 Da LogP 7.80 TPSA 63.6	1 viol.	✓ Clean	`CC(C)CCC[C@@H](C)[C@H]1CC[C@@H]2[C@@]1(CC[C@H]3…`
Z5G	7MET	A0A0B9X4I2	335.8 Da LogP 4.23 TPSA 66.4	✓ Ro5	✓ Clean	`c1cc(ccc1C(=O)Nc2c(c3c(s2)CCCC3)C(=O)O)Cl`

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
ZINC2922863	1.000	335.8 Da LogP 4.23 TPSA 66.4	✓ Ro5	✓ Clean	`O=C(Nc1sc2c(c1C(=O)O)CCCC2)c1ccc(Cl)cc1`
ZINC20334905	0.974	349.8 Da LogP 4.62 TPSA 66.4	✓ Ro5	✓ Clean	`O=C(Nc1sc2c(c1C(=O)O)CCCCC2)c1ccc(Cl)cc1`
ZINC4899186	0.947	321.8 Da LogP 3.84 TPSA 66.4	✓ Ro5	✓ Clean	`O=C(Nc1sc2c(c1C(=O)O)CCC2)c1ccc(Cl)cc1`
ZINC12360002	0.810	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	0.810	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	0.810	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	0.810	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	0.810	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	0.810	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	0.810	427.2 Da LogP -1.75 TPSA 232.6	2 viol.	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@@H](CO[P@@](=O)(O)OP(=…`
ZINC8586019	0.810	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	0.810	427.2 Da LogP -1.75 TPSA 232.6	2 viol.	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@@H](CO[P@@](=O)(O)OP(=…`
ZINC8586021	0.810	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	0.810	427.2 Da LogP -1.75 TPSA 232.6	2 viol.	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@@H](CO[P@@](=O)(O)OP(=…`
ZINC78111	0.800	301.4 Da LogP 3.58 TPSA 66.4	✓ Ro5	✓ Clean	`O=C(Nc1sc2c(c1C(=O)O)CCCC2)c1ccccc1`
ZINC127403	0.786	319.4 Da LogP 3.72 TPSA 66.4	✓ Ro5	✓ Clean	`O=C(Nc1sc2c(c1C(=O)O)CCCC2)c1ccc(F)cc1`
ZINC188404	0.786	315.4 Da LogP 3.89 TPSA 66.4	✓ Ro5	✓ Clean	`Cc1ccc(C(=O)Nc2sc3c(c2C(=O)O)CCCC3)cc1`
ZINC2591233	0.786	334.8 Da LogP 3.63 TPSA 72.2	✓ Ro5	✓ Clean	`NC(=O)c1c(NC(=O)c2ccc(Cl)cc2)sc2c1CCCC2`
ZINC8387400	0.786	427.3 Da LogP 4.18 TPSA 66.4	✓ Ro5	✓ Clean	`O=C(Nc1sc2c(c1C(=O)O)CCCC2)c1ccc(I)cc1`
ZINC210056	0.780	315.4 Da LogP 3.97 TPSA 66.4	✓ Ro5	✓ Clean	`O=C(Nc1sc2c(c1C(=O)O)CCCCC2)c1ccccc1`
ZINC1218717	0.767	362.9 Da LogP 4.41 TPSA 72.2	✓ Ro5	✓ Clean	`NC(=O)c1c(NC(=O)c2ccc(Cl)cc2)sc2c1CCCCCC2`
ZINC2158336	0.767	357.5 Da LogP 4.87 TPSA 66.4	✓ Ro5	✓ Clean	`CC(C)(C)c1ccc(C(=O)Nc2sc3c(c2C(=O)O)CCCC3)cc1`
ZINC35587	0.767	348.9 Da LogP 4.02 TPSA 72.2	✓ Ro5	✓ Clean	`NC(=O)c1c(NC(=O)c2ccc(Cl)cc2)sc2c1CCCCC2`
ZINC4348733	0.767	348.9 Da LogP 3.89 TPSA 58.2	✓ Ro5	✓ Clean	`CNC(=O)c1c(NC(=O)c2ccc(Cl)cc2)sc2c1CCCC2`
ZINC125918	0.756	287.3 Da LogP 3.19 TPSA 66.4	✓ Ro5	✓ Clean	`O=C(Nc1sc2c(c1C(=O)O)CCC2)c1ccccc1`
ZINC124138	0.750	349.8 Da LogP 4.32 TPSA 55.4	✓ Ro5	✓ Clean	`COC(=O)c1c(NC(=O)c2ccc(Cl)cc2)sc2c1CCCC2`
ZINC146439	0.744	320.8 Da LogP 3.24 TPSA 72.2	✓ Ro5	✓ Clean	`NC(=O)c1c(NC(=O)c2ccc(Cl)cc2)sc2c1CCC2`
ZINC2157576	0.744	366.2 Da LogP 3.95 TPSA 66.4	✓ Ro5	✓ Clean	`O=C(Nc1sc2c(c1C(=O)O)CCC2)c1ccc(Br)cc1`
ZINC349870	0.744	305.3 Da LogP 3.33 TPSA 66.4	✓ Ro5	✓ Clean	`O=C(Nc1sc2c(c1C(=O)O)CCC2)c1ccc(F)cc1`
ZINC8387402	0.744	413.2 Da LogP 3.79 TPSA 66.4	✓ Ro5	✓ Clean	`O=C(Nc1sc2c(c1C(=O)O)CCC2)c1ccc(I)cc1`
ZINC13518964	0.741	347.2 Da LogP -1.86 TPSA 186.1	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@@H](COP(=O)(O)O)[C@H](…`
ZINC1532515	0.741	347.2 Da LogP -1.86 TPSA 186.1	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@H]1O[C@@H](COP(=O)(O)O)[C@H](O…`
ZINC1571045	0.741	347.2 Da LogP -1.86 TPSA 186.1	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@@H](COP(=O)(O)O)[C@@H]…`
ZINC1842158	0.741	347.2 Da LogP -1.86 TPSA 186.1	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@H]1O[C@@H](COP(=O)(O)O)[C@H](O…`
ZINC2046931	0.741	347.2 Da LogP -1.86 TPSA 186.1	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@@H](COP(=O)(O)O)[C@H](…`
ZINC2126310	0.741	347.2 Da LogP -1.86 TPSA 186.1	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](COP(=O)(O)O)[C@@H](…`
ZINC3201891	0.741	347.2 Da LogP -1.86 TPSA 186.1	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@@H](COP(=O)(O)O)[C@@H]…`
ZINC3201893	0.741	347.2 Da LogP -1.86 TPSA 186.1	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@H]1O[C@@H](COP(=O)(O)O)[C@@H](…`
ZINC3830180	0.741	347.2 Da LogP -1.86 TPSA 186.1	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@H]1O[C@@H](COP(=O)(O)O)[C@@H](…`
ZINC3860156	0.741	347.2 Da LogP -1.86 TPSA 186.1	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](COP(=O)(O)O)[C@@H](…`
ZINC3977897	0.741	347.2 Da LogP -1.86 TPSA 186.1	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@H]1O[C@H](COP(=O)(O)O)[C@@H](O…`
ZINC4806442	0.741	347.2 Da LogP -1.86 TPSA 186.1	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](COP(=O)(O)O)[C@H](O…`
ZINC8613167	0.741	347.2 Da LogP -1.86 TPSA 186.1	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](COP(=O)(O)O)[C@H](O…`
ZINC888095786	0.739	350.8 Da LogP 3.39 TPSA 78.4	✓ Ro5	✓ Clean	`O=C(Nc1sc2c(c1C(=O)O)CCCNC2)c1ccc(Cl)cc1`
ZINC1200205	0.733	363.9 Da LogP 4.71 TPSA 55.4	✓ Ro5	✓ Clean	`COC(=O)c1c(NC(=O)c2ccc(Cl)cc2)sc2c1CCCCC2`
ZINC227470	0.733	335.8 Da LogP 4.23 TPSA 66.4	✓ Ro5	✓ Clean	`O=C(Nc1sc2c(c1C(=O)O)CCCC2)c1cccc(Cl)c1`
ZINC3148790	0.733	331.4 Da LogP 3.59 TPSA 75.6	✓ Ro5	✓ Clean	`COc1ccc(C(=O)Nc2sc3c(c2C(=O)O)CCCC3)cc1`
ZINC315655645	0.733	336.8 Da LogP 3.63 TPSA 79.3	✓ Ro5	✓ Clean	`O=C(Nc1sc2c(c1C(=O)O)CCCC2)c1ccc(Cl)cn1`
ZINC4096224	0.729	346.2 Da LogP -1.90 TPSA 191.9	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](CO[P@](N)(=O)O)[C@@…`
ZINC5055668	0.727	334.8 Da LogP 3.50 TPSA 58.2	✓ Ro5	✓ Clean	`CNC(=O)c1c(NC(=O)c2ccc(Cl)cc2)sc2c1CCC2`

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.