Protein profile

VK055_5123

ABC transporter family protein

Genome: KpATCC43816

Gene: ybtP AIK83649.1 Structure source: AlphaFold + ColabFold UniProt A0A0H3GV18

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Amino acids 570

Annotations 6

Features 46

PDB binders 4

Druggability 0.764

Overview

Basic information about this protein and its source genome.

Accession: VK055_5123
Assembly: Klebsiella pneumoniae subsp. pneumoniae strain ATCC 43816 KPPR1, complete genome
Gene: ybtP AIK83649.1
Status: annotated
Amino acids: 570
Structure source: AlphaFold + ColabFold

GO:0005524 Binding to ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator. GO:0016020 A lipid bilayer along with all the proteins and protein complexes embedded in it and attached to it. 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: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:0005886 The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.

Target profile

Computed evidence for target prioritization.

Human off-target: hit
Human identity (%): 56.164
Human E-value: 1.69e-19
Gut microbiome off-target: hit
Essential (DEG): N
DEG identity (%): 50.0
Localization: CytoplasmicMembrane
ColabFold pLDDT: 88.58

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 0.764

Structure A0A0H3GV18

Pocket Pocket 2

P2Rank 0.216

Structure A0A0H3GV18

Pocket Pocket 1

ColabFold model

FPocket 0.493 · Pocket 7

P2Rank 0.36 · Pocket 1

Core conservation Accessory gene

Roary accessory

CoreCruncher accessory

Gut microbiome 7 / 4744 genomes with a hit

Normalized 0.001

Sequence

Primary amino-acid sequence viewer.

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

6 GO

Gene Ontology (GO)

GO:0005524 Binding to ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
GO:0016020 A lipid bilayer along with all the proteins and protein complexes embedded in it and attached to it.
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: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:0005886 The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.

Sequence Features

Domain/signature hits from InterPro and related databases.

46 records

Show feature table

Start	End	DB	Term	Name
138	154	Phobius	TRANSMEMBRANE	Region of a membrane-bound protein predicted to be embedded in the membrane.
1	281	ProSiteProfiles	PS50929	ABC transporter integral membrane type-1 fused domain profile.
1	281	InterPro	IPR011527	ABC transporter type 1, transmembrane domain
18	21	Phobius	SIGNAL_PEPTIDE_C_REGION	C-terminal region of a signal peptide.
31	50	TMHMM	TMhelix	Region of a membrane-bound protein predicted to be embedded in the membrane.
221	243	TMHMM	TMhelix	Region of a membrane-bound protein predicted to be embedded in the membrane.
41	547	PANTHER	PTHR24222	ABC TRANSPORTER B FAMILY
41	547	InterPro	IPR039421	Type 1 protein exporter
241	251	Phobius	NON_CYTOPLASMIC_DOMAIN	Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
2	17	Phobius	SIGNAL_PEPTIDE_H_REGION	Hydrophobic region of a signal peptide.
253	275	TMHMM	TMhelix	Region of a membrane-bound protein predicted to be embedded in the membrane.
303	556	FunFam	G3DSA:3.40.50.300:FF:000221	Multidrug ABC transporter ATP-binding protein
51	113	Phobius	CYTOPLASMIC_DOMAIN	Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
2	301	SUPERFAMILY	SSF90123	ABC transporter transmembrane region
2	301	InterPro	IPR036640	ABC transporter type 1, transmembrane domain superfamily
1	298	Gene3D	G3DSA:1.20.1560.10	ABC transporter type 1, transmembrane domain
1	298	InterPro	IPR036640	ABC transporter type 1, transmembrane domain superfamily
339	533	SMART	SM00382	AAA_5
339	533	InterPro	IPR003593	AAA+ ATPase domain
276	570	Phobius	CYTOPLASMIC_DOMAIN	Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
113	132	TMHMM	TMhelix	Region of a membrane-bound protein predicted to be embedded in the membrane.
307	549	SUPERFAMILY	SSF52540	P-loop containing nucleoside triphosphate hydrolases
307	549	InterPro	IPR027417	P-loop containing nucleoside triphosphate hydrolase
31	50	Phobius	TRANSMEMBRANE	Region of a membrane-bound protein predicted to be embedded in the membrane.
133	137	Phobius	NON_CYTOPLASMIC_DOMAIN	Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
1	21	Phobius	SIGNAL_PEPTIDE	Signal peptide region
303	558	Gene3D	G3DSA:3.40.50.300	-
303	558	InterPro	IPR027417	P-loop containing nucleoside triphosphate hydrolase
1	27	SignalP_EUK	SignalP-TM	SignalP-TM
39	248	Pfam	PF00664	ABC transporter transmembrane region
39	248	InterPro	IPR011527	ABC transporter type 1, transmembrane domain
155	218	Phobius	CYTOPLASMIC_DOMAIN	Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
312	548	ProSiteProfiles	PS50893	ATP-binding cassette, ABC transporter-type domain profile.
312	548	InterPro	IPR003439	ABC transporter-like, ATP-binding domain
114	132	Phobius	TRANSMEMBRANE	Region of a membrane-bound protein predicted to be embedded in the membrane.
219	240	Phobius	TRANSMEMBRANE	Region of a membrane-bound protein predicted to be embedded in the membrane.
451	465	ProSitePatterns	PS00211	ABC transporters family signature.
451	465	InterPro	IPR017871	ABC transporter-like, conserved site
22	30	Phobius	NON_CYTOPLASMIC_DOMAIN	Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
1	289	CDD	cd07346	ABC_6TM_exporters
252	275	Phobius	TRANSMEMBRANE	Region of a membrane-bound protein predicted to be embedded in the membrane.
1	1	Phobius	SIGNAL_PEPTIDE_N_REGION	N-terminal region of a signal peptide.
2	21	TMHMM	TMhelix	Region of a membrane-bound protein predicted to be embedded in the membrane.
330	479	Pfam	PF00005	ABC transporter
330	479	InterPro	IPR003439	ABC transporter-like, ATP-binding domain
136	154	TMHMM	TMhelix	Region of a membrane-bound protein predicted to be embedded in the membrane.

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_A0A0H3GV18	AlphaFold	—	—	full sequence	—	Viewing
ColabFold VK055_5123	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
2				0.764
5				0.358
10				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	3.19	0.109
2	2.92	0.093
3	1.94	0.04
4	1.72	0.03
5	1.55	0.023

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
7				0.493
4				0.337
11				0.295

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	4.84	0.216
2	3.24	0.112
3	2.5	0.069
4	2.23	0.055
5	2.06	0.046

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
0SA	4F4C	P34712	512.7 Da LogP -0.13 TPSA 169.3	3 viol.	✓ Clean	`CCCCCCCCCCCS[C@H]1[C@@H]([C@H]([C@@H]([C@H](O1)…`
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)…`
O34	6P6J	Q1RAG2	481.7 Da LogP 2.66 TPSA 114.5	✓ Ro5	✓ Clean	`C[C@@]1(CSC(=N1)C(C)(C)[C@@H]([C@@H]2CS[C@@H](N…`

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
ZINC100053481	1.000	484.6 Da LogP -0.91 TPSA 169.3	2 viol.	✓ Clean	`CCCCCCCCCS[C@@H]1O[C@H](CO)[C@@H](O[C@@H]2O[C@H…`
ZINC100057932	1.000	498.6 Da LogP -0.52 TPSA 169.3	2 viol.	✓ Clean	`CCCCCCCCCCS[C@@H]1O[C@H](CO)[C@@H](O[C@@H]2O[C@…`
ZINC100058001	1.000	470.6 Da LogP -1.30 TPSA 169.3	2 viol.	✓ Clean	`CCCCCCCCS[C@@H]1O[C@H](CO)[C@@H](O[C@H]2O[C@H](…`
ZINC100796989	1.000	484.6 Da LogP -0.91 TPSA 169.3	2 viol.	✓ Clean	`CCCCCCCCCS[C@@H]1O[C@H](CO)[C@@H](O[C@H]2O[C@H]…`
ZINC14114498	1.000	498.6 Da LogP -0.52 TPSA 169.3	2 viol.	✓ Clean	`CCCCCCCCCCS[C@@H]1O[C@H](CO)[C@@H](O[C@H]2O[C@H…`
ZINC12360002	0.855	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	0.855	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	0.855	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	0.855	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	0.855	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	0.855	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	0.855	427.2 Da LogP -1.75 TPSA 232.6	2 viol.	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@@H](CO[P@@](=O)(O)OP(=…`
ZINC8586019	0.855	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	0.855	427.2 Da LogP -1.75 TPSA 232.6	2 viol.	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@@H](CO[P@@](=O)(O)OP(=…`
ZINC8586021	0.855	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	0.855	427.2 Da LogP -1.75 TPSA 232.6	2 viol.	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@@H](CO[P@@](=O)(O)OP(=…`
ZINC13518964	0.782	347.2 Da LogP -1.86 TPSA 186.1	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@@H](COP(=O)(O)O)[C@H](…`
ZINC1532515	0.782	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	0.782	347.2 Da LogP -1.86 TPSA 186.1	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@@H](COP(=O)(O)O)[C@@H]…`
ZINC1842158	0.782	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	0.782	347.2 Da LogP -1.86 TPSA 186.1	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@@H](COP(=O)(O)O)[C@H](…`
ZINC2126310	0.782	347.2 Da LogP -1.86 TPSA 186.1	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](COP(=O)(O)O)[C@@H](…`
ZINC3201891	0.782	347.2 Da LogP -1.86 TPSA 186.1	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@@H](COP(=O)(O)O)[C@@H]…`
ZINC3201893	0.782	347.2 Da LogP -1.86 TPSA 186.1	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@H]1O[C@@H](COP(=O)(O)O)[C@@H](…`
ZINC3830180	0.782	347.2 Da LogP -1.86 TPSA 186.1	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@H]1O[C@@H](COP(=O)(O)O)[C@@H](…`
ZINC3860156	0.782	347.2 Da LogP -1.86 TPSA 186.1	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](COP(=O)(O)O)[C@@H](…`
ZINC3977897	0.782	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	0.782	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	0.782	347.2 Da LogP -1.86 TPSA 186.1	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](COP(=O)(O)O)[C@H](O…`
ZINC4096224	0.768	346.2 Da LogP -1.90 TPSA 191.9	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](CO[P@](N)(=O)O)[C@@…`
ZINC12503850	0.763	427.3 Da LogP -2.04 TPSA 229.4	1 viol.	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](CO[P@](=O)(O)OS(=O)…`
ZINC141161066	0.763	427.3 Da LogP -2.04 TPSA 229.4	1 viol.	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](CO[P@](=O)(O)OS(=O)…`
ZINC141163786	0.763	427.3 Da LogP -2.04 TPSA 229.4	1 viol.	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](CO[P@](=O)(O)OS(=O)…`
ZINC4228246	0.763	427.3 Da LogP -2.04 TPSA 229.4	1 viol.	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](CO[P@@](=O)(O)OS(=O…`
ZINC105372833	0.750	345.3 Da LogP -1.93 TPSA 197.6	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](COP(N)(N)=O)[C@H](O…`
ZINC105372837	0.750	345.3 Da LogP -1.93 TPSA 197.6	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](COP(N)(N)=O)[C@H](O…`
ZINC17107643	0.750	345.3 Da LogP -1.93 TPSA 197.6	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](COP(N)(N)=O)[C@@H](…`
ZINC204538551	0.750	345.3 Da LogP -1.93 TPSA 197.6	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](COP(N)(N)=O)[C@@H](…`
ZINC31475423	0.738	434.3 Da LogP -2.99 TPSA 238.4	2 viol.	✓ Clean	`Nc1ncnc2c1ncn2[C@H]1O[C@H](CO[P@@](=O)(O)OC(=O)…`
ZINC100056955	0.732	322.5 Da LogP 1.27 TPSA 90.2	✓ Ro5	✓ Clean	`CCCCCCCCCS[C@@H]1O[C@H](CO)[C@@H](O)[C@H](O)[C@…`
ZINC100056957	0.732	336.5 Da LogP 1.66 TPSA 90.2	✓ Ro5	✓ Clean	`CCCCCCCCCCS[C@@H]1O[C@H](CO)[C@@H](O)[C@H](O)[C…`
ZINC100759478	0.732	308.4 Da LogP 0.88 TPSA 90.2	✓ Ro5	✓ Clean	`CCCCCCCCS[C@@H]1O[C@H](CO)[C@H](O)[C@H](O)[C@@H…`
ZINC101659921	0.732	308.4 Da LogP 0.88 TPSA 90.2	✓ Ro5	✓ Clean	`CCCCCCCCS[C@@H]1O[C@H](CO)[C@H](O)[C@H](O)[C@H]…`
ZINC6845558	0.732	308.4 Da LogP 0.88 TPSA 90.2	✓ Ro5	✓ Clean	`CCCCCCCCS[C@@H]1O[C@H](CO)[C@@H](O)[C@H](O)[C@H…`
ZINC76945567	0.732	308.4 Da LogP 0.88 TPSA 90.2	✓ Ro5	✓ Clean	`CCCCCCCCS[C@@H]1O[C@H](CO)[C@H](O)[C@@H](O)[C@@…`
ZINC77293255	0.732	294.4 Da LogP 0.49 TPSA 90.2	✓ Ro5	✓ Clean	`CCCCCCCS[C@@H]1O[C@@H](CO)[C@@H](O)[C@H](O)[C@H…`
ZINC77293258	0.732	294.4 Da LogP 0.49 TPSA 90.2	✓ Ro5	✓ Clean	`CCCCCCCS[C@@H]1O[C@@H](CO)[C@@H](O)[C@H](O)[C@@…`
ZINC77293261	0.732	294.4 Da LogP 0.49 TPSA 90.2	✓ Ro5	✓ Clean	`CCCCCCCS[C@@H]1O[C@H](CO)[C@@H](O)[C@H](O)[C@@H…`
ZINC85479681	0.732	308.4 Da LogP 0.88 TPSA 90.2	✓ Ro5	✓ Clean	`CCCCCCCCS[C@H]1O[C@H](CO)[C@@H](O)[C@H](O)[C@H]…`
ZINC97943321	0.732	308.4 Da LogP 0.88 TPSA 90.2	✓ Ro5	✓ Clean	`CCCCCCCCS[C@@H]1O[C@H](CO)[C@H](O)[C@@H](O)[C@H…`

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.