Protein profile

VK055_4188

bacterial extracellular solute-binding, 5 Middlefamily protein

Genome: KpATCC43816

Gene: AIK82733.1 Structure source: AlphaFold + ColabFold UniProt A0ABD7NX05

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Amino acids 507

Annotations 3

Features 11

PDB binders 6

Druggability 0.603

Overview

Basic information about this protein and its source genome.

Accession: VK055_4188
Assembly: Klebsiella pneumoniae subsp. pneumoniae strain ATCC 43816 KPPR1, complete genome
Gene: AIK82733.1
Status: annotated
Amino acids: 507
Structure source: AlphaFold + ColabFold

GO:0043190 A complex for the transport of metabolites into and out of the cell, typically comprised of four domains; two membrane-associated domains and two ATP-binding domains at the intracellular face of the membrane, that form a central pore through the plasma membrane. Each of the four core domains may be encoded as a separate polypeptide or the domains can be fused in any one of a number of ways into multidomain polypeptides. In Bacteria and Archaebacteria, ABC transporters also include substrate binding proteins to bind substrate external to the cytoplasm and deliver it to the transporter. GO:0055085 The process in which a solute is transported across a lipid bilayer, from one side of a membrane to the other. GO:0030288 The region between the inner (cytoplasmic or plasma) membrane and outer membrane of organisms with two membranes such as Gram negative bacteria. These periplasmic spaces are relatively thick and contain a thin peptidoglycan layer (PGL), also referred to as a thin cell wall.

Target profile

Computed evidence for target prioritization.

Human off-target: No hit
Human identity (%): 0.0
Gut microbiome off-target: hit
Essential (DEG): N
DEG identity (%): 29.082
Localization: Periplasmic
ColabFold pLDDT: 93.48

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 0.603

Structure A0ABD7NX05

Pocket Pocket 10

P2Rank 0.833

Structure A0ABD7NX05

Pocket Pocket 1

ColabFold model

FPocket 0.261 · Pocket 5

P2Rank 0.952 · Pocket 1

Core conservation Accessory gene

Roary accessory

CoreCruncher accessory

Gut microbiome 45 / 4744 genomes with a hit

Normalized 0.009

Sequence

Primary amino-acid sequence viewer.

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

3 GO

Gene Ontology (GO)

GO:0043190 A complex for the transport of metabolites into and out of the cell, typically comprised of four domains; two membrane-associated domains and two ATP-binding domains at the intracellular face of the membrane, that form a central pore through the plasma membrane. Each of the four core domains may be encoded as a separate polypeptide or the domains can be fused in any one of a number of ways into multidomain polypeptides. In Bacteria and Archaebacteria, ABC transporters also include substrate binding proteins to bind substrate external to the cytoplasm and deliver it to the transporter.
GO:0055085 The process in which a solute is transported across a lipid bilayer, from one side of a membrane to the other.
GO:0030288 The region between the inner (cytoplasmic or plasma) membrane and outer membrane of organisms with two membranes such as Gram negative bacteria. These periplasmic spaces are relatively thick and contain a thin peptidoglycan layer (PGL), also referred to as a thin cell wall.

Sequence Features

Domain/signature hits from InterPro and related databases.

11 records

Show feature table

Start	End	DB	Term	Name
1	496	PIRSF	PIRSF002741	MppA
1	496	InterPro	IPR030678	Peptide/nickel binding protein, MppA-type
14	480	PANTHER	PTHR30290	PERIPLASMIC BINDING COMPONENT OF ABC TRANSPORTER
14	480	InterPro	IPR039424	Solute-binding protein family 5
56	407	Pfam	PF00496	Bacterial extracellular solute-binding proteins, family 5 Middle
56	407	InterPro	IPR000914	Solute-binding protein family 5 domain
25	231	Gene3D	G3DSA:3.40.190.10	-
232	475	Gene3D	G3DSA:3.10.105.10	-
232	474	FunFam	G3DSA:3.10.105.10:FF:000009	ABC transporter substrate-binding protein
13	483	CDD	cd08518	PBP2_NikA_DppA_OppA_like_19
8	480	SUPERFAMILY	SSF53850	Periplasmic binding protein-like II

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_A0ABD7NX05	AlphaFold	—	—	full sequence	—	Viewing
ColabFold VK055_4188	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
10				0.603
14				0.001
32				0.0

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	22.85	0.833
2	17.06	0.716
3	6.88	0.296
4	4.1	0.135
5	2.88	0.073

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
5				0.261
11				0.003
2				0.0

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	42.25	0.952
2	6.23	0.259
3	3.56	0.105
4	1.88	0.031
5	1.44	0.016

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.

56 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
8UX	5YH8	Q2FVE7	328.3 Da LogP -1.10 TPSA 164.6	1 viol.	✓ Clean	`C[C@@H](C(=O)O)N[C@@H](CCN[C@H](Cc1c[nH]cn1)C(=…`
N72	6TFQ	O50271	309.3 Da LogP -3.46 TPSA 184.6	1 viol.	✓ Clean	`C(CC(=O)O)[C@H](C(=O)O)NCC(=O)[C@@H]([C@@H]([C@…`
N7T	6TFS	O50271	309.3 Da LogP -3.46 TPSA 184.6	1 viol.	✓ Clean	`C(CC(=O)O)[C@@H](C(=O)O)NCC(=O)[C@H]([C@@H]([C@…`
NGE	5YYB	Q7VL18	325.3 Da LogP -4.90 TPSA 197.0	1 viol.	✓ Clean	`C1[C@@H]([C@H]([C@@H](O[C@@]1(C(=O)O)O)[C@@H]([…`
OXL	4OEV	Q0P844	88.0 Da LogP -3.51 TPSA 80.3	✓ Ro5	✓ Clean	`C(=O)(C(=O)[O-])[O-]`
SLB	5Z99	Q7VL18	309.3 Da LogP -3.87 TPSA 176.8	1 viol.	✓ Clean	`CC(=O)N[C@@H]1[C@H](C[C@](O[C@H]1[C@@H]([C@@H](…`

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
ZINC106403632	1.000	325.3 Da LogP -4.90 TPSA 197.0	1 viol.	✓ Clean	`O=C(CO)N[C@H]1[C@@H]([C@H](O)[C@H](O)CO)O[C@@](…`
ZINC12359995	1.000	309.3 Da LogP -3.87 TPSA 176.8	1 viol.	✓ Clean	`CC(=O)N[C@@H]1[C@H](O)C[C@](O)(C(=O)O)O[C@H]1[C…`
ZINC15206143	1.000	309.3 Da LogP -3.87 TPSA 176.8	1 viol.	✓ Clean	`CC(=O)N[C@H]1[C@@H]([C@@H](O)[C@@H](O)CO)O[C@@]…`
ZINC15206146	1.000	309.3 Da LogP -3.87 TPSA 176.8	1 viol.	✓ Clean	`CC(=O)N[C@H]1[C@@H]([C@H](O)[C@@H](O)CO)O[C@@](…`
ZINC15206149	1.000	309.3 Da LogP -3.87 TPSA 176.8	1 viol.	✓ Clean	`CC(=O)N[C@@H]1[C@H](O)C[C@](O)(C(=O)O)O[C@H]1[C…`
ZINC1532591	1.000	309.3 Da LogP -3.87 TPSA 176.8	1 viol.	✓ Clean	`CC(=O)N[C@@H]1[C@@H]([C@H](O)[C@H](O)CO)O[C@@](…`
ZINC247362640	1.000	325.3 Da LogP -4.90 TPSA 197.0	1 viol.	✓ Clean	`O=C(CO)N[C@H]1[C@@H]([C@H](O)[C@@H](O)CO)O[C@@]…`
ZINC247362642	1.000	325.3 Da LogP -4.90 TPSA 197.0	1 viol.	✓ Clean	`O=C(CO)N[C@H]1[C@@H]([C@@H](O)[C@@H](O)CO)O[C@@…`
ZINC247362655	1.000	325.3 Da LogP -4.90 TPSA 197.0	1 viol.	✓ Clean	`O=C(CO)N[C@H]1[C@@H]([C@@H](O)[C@H](O)CO)O[C@@]…`
ZINC2586055	1.000	309.3 Da LogP -3.87 TPSA 176.8	1 viol.	✓ Clean	`CC(=O)N[C@H]1[C@@H](O)C[C@](O)(C(=O)O)O[C@@H]1[…`
ZINC3793840	1.000	309.3 Da LogP -3.87 TPSA 176.8	1 viol.	✓ Clean	`CC(=O)N[C@@H]1[C@@H](O)C[C@@](O)(C(=O)O)O[C@H]1…`
ZINC3870085	1.000	309.3 Da LogP -3.87 TPSA 176.8	1 viol.	✓ Clean	`CC(=O)N[C@H]1[C@@H]([C@H](O)[C@H](O)CO)O[C@@](O…`
ZINC3870086	1.000	309.3 Da LogP -3.87 TPSA 176.8	1 viol.	✓ Clean	`CC(=O)N[C@@H]1[C@@H](O)C[C@](O)(C(=O)O)O[C@@H]1…`
ZINC4081651	1.000	309.3 Da LogP -3.87 TPSA 176.8	1 viol.	✓ Clean	`CC(=O)N[C@@H]1[C@@H](O)C[C@](O)(C(=O)O)O[C@H]1[…`
ZINC4096097	1.000	325.3 Da LogP -4.90 TPSA 197.0	1 viol.	✓ Clean	`O=C(CO)N[C@@H]1[C@@H](O)C[C@@](O)(C(=O)O)O[C@H]…`
ZINC4293691	1.000	309.3 Da LogP -3.87 TPSA 176.8	1 viol.	✓ Clean	`CC(=O)N[C@@H]1[C@@H](O)C[C@@](O)(C(=O)O)O[C@@H]…`
ZINC43509538	1.000	309.3 Da LogP -3.87 TPSA 176.8	1 viol.	✓ Clean	`CC(=O)N[C@H]1[C@@H](O)C[C@@](O)(C(=O)O)O[C@H]1[…`
ZINC44790306	1.000	309.3 Da LogP -3.87 TPSA 176.8	1 viol.	✓ Clean	`CC(=O)N[C@@H]1[C@@H](O)C[C@](O)(C(=O)O)O[C@@H]1…`
ZINC5227885	1.000	309.3 Da LogP -3.87 TPSA 176.8	1 viol.	✓ Clean	`CC(=O)N[C@@H]1[C@H](O)C[C@](O)(C(=O)O)O[C@H]1[C…`
ZINC71789682	1.000	309.3 Da LogP -3.87 TPSA 176.8	1 viol.	✓ Clean	`CC(=O)N[C@@H]1[C@@H](O)C[C@](O)(C(=O)O)O[C@@H]1…`
ZINC71789683	1.000	309.3 Da LogP -3.87 TPSA 176.8	1 viol.	✓ Clean	`CC(=O)N[C@@H]1[C@@H](O)C[C@](O)(C(=O)O)O[C@@H]1…`
ZINC71789800	1.000	309.3 Da LogP -3.87 TPSA 176.8	1 viol.	✓ Clean	`CC(=O)N[C@H]1[C@@H]([C@@H](O)[C@H](O)CO)O[C@@](…`
ZINC71789801	1.000	309.3 Da LogP -3.87 TPSA 176.8	1 viol.	✓ Clean	`CC(=O)N[C@@H]1[C@H](O)C[C@](O)(C(=O)O)O[C@H]1[C…`
ZINC79036671	1.000	309.3 Da LogP -3.46 TPSA 184.6	1 viol.	✓ Clean	`O=C(O)CC[C@H](NCC(=O)[C@@H](O)[C@H](O)[C@H](O)C…`
ZINC33977700	0.818	308.3 Da LogP -3.91 TPSA 182.6	1 viol.	✓ Clean	`CC(=O)N[C@@H]1[C@@H](O)C[C@@](O)(C(=O)O)O[C@H]1…`
ZINC100655903	0.783	323.3 Da LogP -3.78 TPSA 165.8	1 viol.	✓ Clean	`COC(=O)[C@]1(O)C[C@H](O)[C@H](NC(C)=O)[C@H]([C@…`
ZINC100655904	0.783	323.3 Da LogP -3.78 TPSA 165.8	1 viol.	✓ Clean	`COC(=O)[C@]1(O)C[C@H](O)[C@H](NC(C)=O)[C@H]([C@…`
ZINC100655906	0.783	323.3 Da LogP -3.78 TPSA 165.8	1 viol.	✓ Clean	`COC(=O)[C@]1(O)C[C@H](O)[C@H](NC(C)=O)[C@H]([C@…`
ZINC146216515	0.783	323.3 Da LogP -3.78 TPSA 165.8	1 viol.	✓ Clean	`COC(=O)[C@@]1(O)C[C@@H](O)[C@@H](NC(C)=O)[C@H](…`
ZINC2382416875	0.783	323.3 Da LogP -3.78 TPSA 165.8	1 viol.	✓ Clean	`COC(=O)[C@@]1(O)C[C@H](O)[C@@H](NC(C)=O)[C@H]([…`
ZINC2558706	0.783	323.3 Da LogP -3.78 TPSA 165.8	1 viol.	✓ Clean	`COC(=O)[C@@]1(O)C[C@@H](O)[C@H](NC(C)=O)[C@@H](…`
ZINC2586056	0.783	323.3 Da LogP -3.78 TPSA 165.8	1 viol.	✓ Clean	`COC(=O)[C@@]1(O)C[C@H](O)[C@H](NC(C)=O)[C@@H]([…`
ZINC26254851	0.783	323.3 Da LogP -3.78 TPSA 165.8	1 viol.	✓ Clean	`COC(=O)[C@@]1(O)C[C@H](O)[C@@H](NC(C)=O)[C@H]([…`
ZINC4293695	0.783	323.3 Da LogP -3.78 TPSA 165.8	1 viol.	✓ Clean	`COC(=O)[C@]1(O)C[C@@H](O)[C@@H](NC(C)=O)[C@@H](…`
ZINC4293696	0.783	323.3 Da LogP -3.78 TPSA 165.8	1 viol.	✓ Clean	`COC(=O)[C@]1(O)C[C@H](O)[C@@H](NC(C)=O)[C@@H]([…`
ZINC4293697	0.783	323.3 Da LogP -3.78 TPSA 165.8	1 viol.	✓ Clean	`COC(=O)[C@]1(O)C[C@@H](O)[C@@H](NC(C)=O)[C@H]([…`
ZINC4293698	0.783	323.3 Da LogP -3.78 TPSA 165.8	1 viol.	✓ Clean	`COC(=O)[C@]1(O)C[C@H](O)[C@@H](NC(C)=O)[C@H]([C…`
ZINC43771922	0.783	323.3 Da LogP -3.78 TPSA 165.8	1 viol.	✓ Clean	`COC(=O)[C@]1(O)C[C@H](O)[C@@H](NC(C)=O)[C@H]([C…`
ZINC4533821	0.783	323.3 Da LogP -3.78 TPSA 165.8	1 viol.	✓ Clean	`COC(=O)[C@@]1(O)C[C@@H](O)[C@@H](NC(C)=O)[C@@H]…`
ZINC4533822	0.783	323.3 Da LogP -3.78 TPSA 165.8	1 viol.	✓ Clean	`COC(=O)[C@@]1(O)C[C@H](O)[C@@H](NC(C)=O)[C@@H](…`
ZINC64220345	0.783	323.3 Da LogP -3.78 TPSA 165.8	1 viol.	✓ Clean	`COC(=O)[C@]1(O)C[C@H](O)[C@H](NC(C)=O)[C@H]([C@…`
ZINC76938880	0.783	323.3 Da LogP -3.78 TPSA 165.8	1 viol.	✓ Clean	`COC(=O)[C@]1(O)C[C@@H](O)[C@@H](NC(C)=O)[C@H]([…`
ZINC95635434	0.783	323.3 Da LogP -3.78 TPSA 165.8	1 viol.	✓ Clean	`COC(=O)[C@@]1(O)C[C@@H](O)[C@@H](NC(C)=O)[C@H](…`
ZINC4096286	0.750	351.3 Da LogP -3.30 TPSA 182.8	1 viol.	✓ Clean	`CC(=O)N[C@@H]1[C@@H](O)C[C@@](O)(C(=O)O)O[C@H]1…`
ZINC96327832	0.750	351.3 Da LogP -3.30 TPSA 182.8	1 viol.	✓ Clean	`CC(=O)N[C@@H]1[C@@H](O)C[C@](O)(C(=O)O)O[C@H]1[…`
ZINC16123778	0.694	323.3 Da LogP -3.22 TPSA 165.8	1 viol.	✓ Clean	`CO[C@]1(C(=O)O)C[C@@H](O)[C@@H](NC(C)=O)[C@H]([…`
ZINC247941808	0.694	323.3 Da LogP -3.22 TPSA 165.8	1 viol.	✓ Clean	`CO[C@]1(C(=O)O)C[C@H](O)[C@H](NC(C)=O)[C@H]([C@…`
ZINC4557072	0.694	323.3 Da LogP -3.22 TPSA 165.8	1 viol.	✓ Clean	`CO[C@]1(C(=O)O)C[C@H](O)[C@@H](NC(C)=O)[C@@H]([…`
ZINC5884114	0.694	323.3 Da LogP -3.22 TPSA 165.8	1 viol.	✓ Clean	`CO[C@]1(C(=O)O)C[C@H](O)[C@@H](NC(C)=O)[C@H]([C…`
ZINC76935790	0.694	323.3 Da LogP -3.22 TPSA 165.8	1 viol.	✓ Clean	`CO[C@]1(C(=O)O)C[C@H](O)[C@H](NC(C)=O)[C@H]([C@…`

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.