Protein target profile

KP13_04195

Lipid A export ATP-binding/permease protein msbA

Genome: KpKP13 Gene: AHE45426.1 msbA 3D evidence: AlphaFold DB model + ColabFold model UniProt A0A0H3GV05
Length 582
Pocket druggability 0.97
Direct ligand evidence 0 59 total records
Functional annotation 0 EC 9 GO
Target summary

Promising target candidate with multiple supporting evidence streams.

Automated synthesis of the evidence currently loaded. Review the underlying records before prioritizing this protein.

Terms and data sources used on this page

PDB: experimentally determined structures from the Protein Data Bank. These are the strongest structural evidence, but may cover only part of the protein.

AlphaFold DB model: a precomputed predicted structure downloaded from AlphaFold Database/UniProt, not an experiment performed here.

ColabFold model: a predicted structure generated for this workspace; interpret it with coverage and confidence.

pLDDT: confidence score for predicted structures. High values support local geometry; low values mean the region should not drive pocket interpretation.

FPocket / P2Rank: software tools that predict possible ligand-binding pockets on a 3D structure. They are useful screening signals, not experimental validation.

Druggability: a pocket-based estimate of whether a small molecule could bind productively. It does not mean a drug already exists.

PDB ligand: a compound observed in an experimental structure. Direct same-protein records are stronger than homolog-transferred records.

ChEMBL: a public database of measured compound bioactivity. Direct entries are stronger than entries transferred from similar proteins.

ZINC: a purchasable-compound database. Here it marks proposed candidates from chemical similarity, not measured binders.

LigQ / LigQ_2: an internal Target pipeline step that gathers PDB, ChEMBL, and ZINC ligand evidence for each protein.

Off-target: sequence similarity to proteins we prefer not to hit, such as human proteins or beneficial gut microbiome proteins.

DEG: Database of Essential Genes. A match suggests the protein resembles genes known to be essential in other organisms.

Roary / CoreCruncher: pan-genome tools used to decide whether a gene is core across analyzed strains or accessory/strain-specific.

EC / GO: functional annotations: EC describes enzyme reactions; GO describes biological process, molecular function, or cellular component.

KEGG pathway: a curated metabolic route label used here to group reactions imported from the metabolic model.

Chokepoint: a metabolic reaction that is the only producer or consumer of a metabolite in the imported model.

Prioritization evidence

Selectivity, essentiality, structural confidence, conservation, and predicted binding-site evidence.

Off-target risk

Human off-target
Hit
Human identity (%)
61.039 Lower values reduce human off-target concern.
Human E-value
2.5399999999999998e-24
Gut microbiome similarity
3.1% of screened genomes Lower prevalence suggests narrower overlap with the screened gut microbiome.

Essentiality

Essential (DEG)
Y
DEG identity (%)
92.955 Higher values support similarity to known essential genes.
DEG E-value
0.0 Smaller values mean stronger essential-gene similarity.

Localization

Localization
CytoplasmicMembrane

Structure confidence

ColabFold pLDDT
89.38 0-100 confidence; >70 supports local structural interpretation.

Binding-site evidence

AlphaFold DB / UniProt model

The selected pocket score is the FPocket value used for ranking after applying the curated structure priority. It estimates small-molecule pocket quality; it is not experimental binding evidence. The 3D viewer may show a different loaded structure, so visible pockets can differ.

FPocket 0.97
Structure A0A0H3GV05
Pocket Pocket 1
P2Rank 0.372
Structure A0A0H3GV05
Pocket Pocket 1
ColabFold model
FPocket 0.727 · Pocket 9
P2Rank 0.432 · Pocket 1
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 145 / 4744 genomes with a hit
Prevalence 3.1%

Cross-references

External database identifiers for this protein, its structures, ligands, and metabolic reactions.

Sequence

Primary amino-acid sequence viewer.

MQNDKDLSTWQTFRRLWPIIAPFKAGLIVAAVALVLNAGSDTFMLSLLKPLLDDGFGKTDRSVLLWMPLVVIGLMVLRGITSYISSYCISWVSGKVVMTMRRRLFGHMMGMPVAFFDKQSTGTLLSRITYDSEQVASSSSSALITVVREGASIIGLFVMMFYYSWQLSLILIVLAPIVSVAIRVVSKRFRNISKNMQNTMGQVTTSAEQMLKGHKEVLMFGGQEVETKRFDKVSNKMRLQGMKMVSASSISDPIIQLIASLALAFVLYAASFPSVMDTLTAGTITVVFSSMIALMRPLKSLTNVNAQFQRGMAACQTLFAILDSEQEKDEGTRVIERAKGNLKFENVTFTYPGREVAALRNINLDIPEGKTVALVGRSGSGKSTIASLITRFYDVDEGQILLDGHDLREYKLSSLRDQVALVSQNVHLFNDTVANNIAYARTEEYSREQIEEAARMAYAMDFINKMDNGLDTIIGENGVMLSGGQRQRIAIARALLRNSPILILDEATSALDTESERAIQAALDELQKNRTSLVIAHRLSTIEQADEIVVVEDGRIVERGTHHDLLEHKGVYAQLHKMQFGE

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

9 GO

Gene Ontology (GO)

9
  • 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:0016020 A lipid bilayer along with all the proteins and protein complexes embedded in it and attached to it.
  • 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:0005524 Binding to ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
  • GO:0055085 The process in which a solute is transported across a lipid bilayer, from one side of a membrane to the other.
  • 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:0005886 The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.
  • GO:0015421 Catalysis of the reaction: ATP + H2O + oligopeptide(out) = ADP + phosphate + oligopeptide(in).
  • GO:0042802 Binding to an identical protein or proteins.

Sequence domains and features

Domain and signature matches imported from InterPro and related databases.

46 records
Show feature table
Start End DB Term Name
13 35 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
481 495 ProSitePatterns PS00211 ABC transporters family signature.
481 495 InterPro IPR017871 ABC transporter-like, conserved site
12 582 NCBIfam TIGR02203 lipid A export permease/ATP-binding protein MsbA
12 582 InterPro IPR011917 ABC transporter, lipid A-core flippase, MsbA
333 582 FunFam G3DSA:3.40.50.300:FF:000140 Lipid A export ATP-binding/permease protein MsbA
27 316 CDD cd18552 ABC_6TM_MsbA_like
142 163 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
332 582 Gene3D G3DSA:3.40.50.300 -
332 582 InterPro IPR027417 P-loop containing nucleoside triphosphate hydrolase
245 267 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
1 330 FunFam G3DSA:1.20.1560.10:FF:000008 Lipid A export ATP-binding/permease protein MsbA
1 330 Gene3D G3DSA:1.20.1560.10 ABC transporter type 1, transmembrane domain
1 330 InterPro IPR036640 ABC transporter type 1, transmembrane domain superfamily
144 163 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
71 93 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
94 141 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
342 578 ProSiteProfiles PS50893 ATP-binding cassette, ABC transporter-type domain profile.
342 578 InterPro IPR003439 ABC transporter-like, ATP-binding domain
164 168 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
342 576 CDD cd03251 ABCC_MsbA
368 555 SMART SM00382 AAA_5
368 555 InterPro IPR003593 AAA+ ATPase domain
14 325 SUPERFAMILY SSF90123 ABC transporter transmembrane region
14 325 InterPro IPR036640 ABC transporter type 1, transmembrane domain superfamily
273 277 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
359 509 Pfam PF00005 ABC transporter
359 509 InterPro IPR003439 ABC transporter-like, ATP-binding domain
331 580 SUPERFAMILY SSF52540 P-loop containing nucleoside triphosphate hydrolases
331 580 InterPro IPR027417 P-loop containing nucleoside triphosphate hydrolase
296 582 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
187 253 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
27 297 Pfam PF00664 ABC transporter transmembrane region
27 297 InterPro IPR011527 ABC transporter type 1, transmembrane domain
65 93 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
278 295 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
1 20 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
21 45 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
28 310 ProSiteProfiles PS50929 ABC transporter integral membrane type-1 fused domain profile.
28 310 InterPro IPR011527 ABC transporter type 1, transmembrane domain
5 579 PANTHER PTHR43394 ATP-DEPENDENT PERMEASE MDL1, MITOCHONDRIAL
5 579 InterPro IPR039421 Type 1 protein exporter
169 186 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
254 272 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
167 186 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
46 64 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.

3D structure

Selected loaded structure. Experimental PDB entries may cover only a portion of the sequence; AlphaFold DB and ColabFold models typically cover the full protein but remain computational predictions.

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Pocket score High Medium Low
How colors and pocket overlays are used
Uniform protein color marks the displayed model as a single molecular object.
Experimental PDB structures may be colored by chain to distinguish subunits or copies present in the file.
Pocket colors and alpha spheres are evidence overlays for predicted binding cavities; they are not alternative protein chains.
'Alpha spheres' is FPocket's own cavity-shape geometry, imported when available and aligned with the loaded structure.
'Pocket atoms'/'Predicted site atoms' show the pocket's residue atoms instead: P2Rank reports residues rather than alpha spheres, and FPocket falls back to this when alpha-sphere geometry is unavailable or doesn't align.
'No pocket geometry' means neither alpha spheres nor residue-position data could be found for that pocket; the layer just highlights the same residues as 'Nearby residues'.
Pocket details Inspect a specific pocket, or open the full viewer

Binding pockets · FPocket

Druggability: high ≥ 0.7 · medium 0.4–0.69 · low < 0.4

Site 1 FPocket #1
0.97
Likely same site as P2Rank 1 2.2 Å 13 shared residues 100% of smaller site
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Surrounding area
Site 2 FPocket #27
0.371
Likely same site as P2Rank 1 8.0 Å 2 shared residues 20% of smaller site
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Surrounding area
Site 3 FPocket #8
0.317
Likely same site as P2Rank 3 1.6 Å 8 shared residues 89% of smaller site
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Surrounding area
Site 4 FPocket #7
0.213
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Surrounding area

Binding pockets · P2Rank

Probability: high ≥ 0.5 · medium 0.2–0.49 · low < 0.2

Site 1 P2Rank #1
0.372
Likely same site as FPocket 1 2.2 Å 13 shared residues 100% of smaller site
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Surrounding area
Site 2 P2Rank #2
0.285
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Surrounding area
Site 3 P2Rank #3
0.243
Likely same site as FPocket 8 1.6 Å 8 shared residues 89% of smaller site
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Surrounding area
Site 4 P2Rank #4
0.094
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Surrounding area
Site 5 P2Rank #5
0.042
Likely same site as FPocket 1 6.5 Å 2 shared residues 40% of smaller site
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Surrounding area
All structural evidence 0 experimental · 2 predicted

Structural evidence

0 + 2

Experimental PDB entries plus predicted AlphaFold DB or ColabFold models. Click Switch to display a different loaded structure in the viewer.

Entry Method Resolution Chain Coverage Links Status
AlphaFold DB AF_A0A0H3GV05
AlphaFold DB full sequence Viewing
ColabFold KP13_04195
ColabFold full sequence Loaded

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.

59 records
Chemistry signal

Structural and bioactivity evidence are both available for this target.

Direct evidence 0 same-protein records
Transferred evidence 9 records from similar proteins
Structural ligands 6 0 loaded crystals
Measured bioactivity 3 direct and transferred ChEMBL records
Proposed compounds 50 similarity-based ZINC candidates
Best available ligand signal
0JZ PDB via homolog 687.4 Da · LogP 1.74 · TPSA 126.0 Open detail RCSB PDB
2J8 PDB via homolog Detail RCSB PDB
4C8 PDB via homolog Detail RCSB PDB
AGS PDB via homolog Detail RCSB PDB
ANP PDB via homolog Detail RCSB PDB

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
0JZ RCSB PDB P21447 687.4 Da LogP 1.74 TPSA 126.0 1 viol. ✓ Clean CC(C)[C@@H]1c2nc(c[se]2)C(=O)N[C@@H](c3nc(c[se]…
2J8 RCSB PDB P21447 687.4 Da LogP 1.74 TPSA 126.0 1 viol. ✓ Clean CC(C)[C@H]1c2nc(c[se]2)C(=O)N[C@H](c3nc(c[se]3)…
4C8 RCSB PDB P21447 564.7 Da LogP 7.29 TPSA 9.2 2 viol. ✓ Clean c1cc(c(cc1Br)Br)Oc2c(cc(cc2Br)Br)Br
AGS RCSB PDB 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 RCSB PDB 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)…
Z5G RCSB PDB A0A0B9X4I2 335.8 Da LogP 4.23 TPSA 66.4 ✓ Ro5 ✓ Clean c1cc(ccc1C(=O)Nc2c(c3c(s2)CCCC3)C(=O)O)Cl

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.