Protein profile

VK055_1501

outer membrane protein A

Genome: KpATCC43816

Gene: AIK80121.1 ompA Structure source: Experimental + AlphaFold + ColabFold UniProt P24017

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Amino acids 356

Annotations 6

Features 49

PDB binders 5

Druggability 0.496

Overview

Basic information about this protein and its source genome.

Accession: VK055_1501
Assembly: Klebsiella pneumoniae subsp. pneumoniae strain ATCC 43816 KPPR1, complete genome
Gene: AIK80121.1 ompA
Status: annotated
Amino acids: 356
Structure source: Experimental + AlphaFold + ColabFold

GO:0015288 Enables the transfer of substances, sized less than 1000 Da, from one side of a membrane to the other. The transmembrane portions of porins consist exclusively of beta-strands which form a beta-barrel. They are found in the outer membranes of Gram-negative bacteria, mitochondria, plastids and possibly acid-fast Gram-positive bacteria. GO:0016020 A lipid bilayer along with all the proteins and protein complexes embedded in it and attached to it. GO:0009279 A lipid bilayer that forms the outermost membrane of the cell envelope; enriched in polysaccharide and protein; the outer leaflet of the membrane contains specific lipopolysaccharide structures. GO:0046930 A protein complex providing a discrete opening in a membrane that allows the passage of gases and/or liquids. GO:0034220 A process in which a monoatomic ion is transported across a membrane. Monatomic ions (also called simple ions) are ions consisting of exactly one atom. GO:0039722 A process in which a symbiont interferes with, inhibits or disrupts a toll-like receptor signaling pathway in the host organism. The host is defined as the larger of the organisms involved in a symbiotic interaction.

Target profile

Computed evidence for target prioritization.

Human off-target: No hit
Human identity (%): 0.0
Gut microbiome off-target: hit
Essential (DEG): Y
DEG identity (%): 83.989
DEG E-value: 0.0
Localization: OuterMembrane
ColabFold pLDDT: 77.52

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 0.496

Structure P24017

Pocket Pocket 2

P2Rank 0.135

Structure P24017

Pocket Pocket 1

ColabFold model

FPocket 0.534 · Pocket 18

P2Rank 0.724 · Pocket 1

Core conservation Conserved core gene

Roary core

CoreCruncher core

Gut microbiome 111 / 4744 genomes with a hit

Normalized 0.023

Sequence

Primary amino-acid sequence viewer.

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

6 GO

Gene Ontology (GO)

GO:0015288 Enables the transfer of substances, sized less than 1000 Da, from one side of a membrane to the other. The transmembrane portions of porins consist exclusively of beta-strands which form a beta-barrel. They are found in the outer membranes of Gram-negative bacteria, mitochondria, plastids and possibly acid-fast Gram-positive bacteria.
GO:0016020 A lipid bilayer along with all the proteins and protein complexes embedded in it and attached to it.
GO:0009279 A lipid bilayer that forms the outermost membrane of the cell envelope; enriched in polysaccharide and protein; the outer leaflet of the membrane contains specific lipopolysaccharide structures.
GO:0046930 A protein complex providing a discrete opening in a membrane that allows the passage of gases and/or liquids.
GO:0034220 A process in which a monoatomic ion is transported across a membrane. Monatomic ions (also called simple ions) are ions consisting of exactly one atom.
GO:0039722 A process in which a symbiont interferes with, inhibits or disrupts a toll-like receptor signaling pathway in the host organism. The host is defined as the larger of the organisms involved in a symbiotic interaction.

Sequence Features

Domain/signature hits from InterPro and related databases.

49 records

Show feature table

Start	End	DB	Term	Name
12	223	Gene3D	G3DSA:2.40.160.20	-
1	21	SignalP_GRAM_NEGATIVE	SignalP-noTM	SignalP-noTM
1	348	Hamap	MF_00842	Outer membrane protein A [ompA].
1	348	InterPro	IPR002368	Outer membrane protein, OmpA
12	223	FunFam	G3DSA:2.40.160.20:FF:000003	Outer membrane protein A
267	311	ProSitePatterns	PS01068	OmpA-like domain.
267	311	InterPro	IPR006690	Outer membrane protein, OmpA-like, conserved site
5	16	Phobius	SIGNAL_PEPTIDE_H_REGION	Hydrophobic region of a signal peptide.
220	348	ProSiteProfiles	PS51123	OmpA-like domain profile.
220	348	InterPro	IPR006665	OmpA-like domain
23	204	Pfam	PF01389	OmpA-like transmembrane domain
23	204	InterPro	IPR000498	Outer membrane protein OmpA-like, transmembrane domain
224	346	Gene3D	G3DSA:3.30.1330.60	-
224	346	InterPro	IPR036737	OmpA-like domain superfamily
1	4	Phobius	SIGNAL_PEPTIDE_N_REGION	N-terminal region of a signal peptide.
1	21	SignalP_GRAM_POSITIVE	SignalP-TM	SignalP-TM
265	280	PRINTS	PR01021	OMPA domain signature
265	280	InterPro	IPR006664	Outer membrane protein, bacterial
233	255	PRINTS	PR01021	OMPA domain signature
233	255	InterPro	IPR006664	Outer membrane protein, bacterial
280	296	PRINTS	PR01021	OMPA domain signature
280	296	InterPro	IPR006664	Outer membrane protein, bacterial
224	342	PANTHER	PTHR30329	STATOR ELEMENT OF FLAGELLAR MOTOR COMPLEX
22	356	Phobius	NON_CYTOPLASMIC_DOMAIN	Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
223	344	SUPERFAMILY	SSF103088	OmpA-like
223	344	InterPro	IPR036737	OmpA-like domain superfamily
221	236	PRINTS	PR01022	Outer membrane protein A signature
221	236	InterPro	IPR002368	Outer membrane protein, OmpA
250	269	PRINTS	PR01022	Outer membrane protein A signature
250	269	InterPro	IPR002368	Outer membrane protein, OmpA
112	128	PRINTS	PR01022	Outer membrane protein A signature
112	128	InterPro	IPR002368	Outer membrane protein, OmpA
289	308	PRINTS	PR01022	Outer membrane protein A signature
289	308	InterPro	IPR002368	Outer membrane protein, OmpA
323	336	PRINTS	PR01022	Outer membrane protein A signature
323	336	InterPro	IPR002368	Outer membrane protein, OmpA
189	203	PRINTS	PR01022	Outer membrane protein A signature
189	203	InterPro	IPR002368	Outer membrane protein, OmpA
175	189	PRINTS	PR01022	Outer membrane protein A signature
175	189	InterPro	IPR002368	Outer membrane protein, OmpA
17	21	Phobius	SIGNAL_PEPTIDE_C_REGION	C-terminal region of a signal peptide.
211	348	FunFam	G3DSA:3.30.1330.60:FF:000004	Outer membrane protein A
22	204	SUPERFAMILY	SSF56925	OMPA-like
22	204	InterPro	IPR011250	Outer membrane protein/outer membrane enzyme PagP, beta-barrel
230	344	CDD	cd07185	OmpA_C-like
230	344	InterPro	IPR006665	OmpA-like domain
1	21	Phobius	SIGNAL_PEPTIDE	Signal peptide region
232	327	Pfam	PF00691	OmpA family
232	327	InterPro	IPR006665	OmpA-like domain

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

1 + 2

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

Entry	Method	Resolution	Chain	Coverage	Links	Status
PDB 5NHX	X-ray	1.95 Å	A	35.4% 209-334	PDBe RCSB PDBj File	Viewing
AlphaFold AF_P24017	AlphaFold	—	—	full sequence	—	Loaded
ColabFold VK055_1501	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
3				0.772

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	Sticks	Spheres	Surfaces	Score	Probability	Labels	Zoom	Positions
1				3.63	0.136

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				0.496

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.

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
5GP	5Y61	Q9I4L6	363.2 Da LogP -2.57 TPSA 206.0	1 viol.	✓ Clean	`c1nc2c(n1[C@H]3[C@@H]([C@@H]([C@H](O3)COP(=O)(O…`
7QA	5U1H	P13794	305.3 Da LogP -1.21 TPSA 179.0	1 viol.	✓ Clean	`C[C@H](C(=O)O)NC(=O)[C@H](CCC[C@H](C(=O)O)N)NC(…`
API	3TD4	Q6RYW5	190.2 Da LogP -1.02 TPSA 126.6	✓ Ro5	✓ Clean	`C(C[C@H](C(=O)O)N)C[C@@H](C(=O)O)N`
C8E	1BXW	P0A910	306.4 Da LogP 2.41 TPSA 57.2	✓ Ro5	✓ Clean	`CCCCCCCCOCCOCCOCCOCCO`
SRT	4G88	Q6RYW5	150.1 Da LogP -2.12 TPSA 115.1	✓ Ro5	✓ Clean	`[C@H]([C@H](C(=O)O)O)(C(=O)O)O`

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
ZINC100014200	1.000	494.7 Da LogP 4.02 TPSA 84.8	✓ Ro5	✓ Clean	`CCCCCCCCCCCCOCCOCCOCCOCCOCCOCCOCCO`
ZINC100070166	1.000	290.4 Da LogP 3.17 TPSA 47.9	✓ Ro5	✓ Clean	`CCCCCCCCCCOCCOCCOCCO`
ZINC100310628	1.000	478.7 Da LogP 4.78 TPSA 75.6	✓ Ro5	✓ Clean	`CCCCCCCCCCCCCCOCCOCCOCCOCCOCCOCCO`
ZINC100365196	1.000	302.5 Da LogP 4.71 TPSA 38.7	✓ Ro5	✓ Clean	`CCCCCCCCCCCCCCOCCOCCO`
ZINC101772322	1.000	434.7 Da LogP 4.76 TPSA 66.4	✓ Ro5	✓ Clean	`CCCCCCCCCCCCCCOCCOCCOCCOCCOCCO`
ZINC103600921	1.000	466.7 Da LogP 3.24 TPSA 84.8	✓ Ro5	✓ Clean	`CCCCCCCCCCOCCOCCOCCOCCOCCOCCOCCO`
ZINC12501413	1.000	363.2 Da LogP -2.57 TPSA 206.0	1 viol.	✓ Clean	`Nc1nc2c(ncn2[C@@H]2O[C@H](COP(=O)(O)O)[C@@H](O)…`
ZINC12958448	1.000	363.2 Da LogP -2.57 TPSA 206.0	1 viol.	✓ Clean	`Nc1nc2c(ncn2[C@@H]2O[C@H](COP(=O)(O)O)[C@H](O)[…`
ZINC14880431	1.000	378.6 Da LogP 3.20 TPSA 66.4	✓ Ro5	✓ Clean	`CCCCCCCCCCOCCOCCOCCOCCOCCO`
ZINC14881140	1.000	306.4 Da LogP 2.41 TPSA 57.2	✓ Ro5	✓ Clean	`CCCCCCCCOCCOCCOCCOCCO`
ZINC1532555	1.000	363.2 Da LogP -2.57 TPSA 206.0	1 viol.	✓ Clean	`Nc1nc2c(ncn2[C@H]2O[C@@H](COP(=O)(O)O)[C@H](O)[…`
ZINC16051619	1.000	350.5 Da LogP 2.42 TPSA 66.4	✓ Ro5	✓ Clean	`CCCCCCCCOCCOCCOCCOCCOCCO`
ZINC16546189	1.000	363.2 Da LogP -2.57 TPSA 206.0	1 viol.	✓ Clean	`Nc1nc2c(ncn2[C@@H]2O[C@H](COP(=O)(O)O)[C@H](O)[…`
ZINC2159505	1.000	363.2 Da LogP -2.57 TPSA 206.0	1 viol.	✓ Clean	`Nc1nc2c(ncn2[C@@H]2O[C@H](COP(=O)(O)O)[C@@H](O)…`
ZINC2584424	1.000	218.3 Da LogP 2.37 TPSA 38.7	✓ Ro5	✓ Clean	`CCCCCCCCOCCOCCO`
ZINC3073318	1.000	363.2 Da LogP -2.57 TPSA 206.0	1 viol.	✓ Clean	`Nc1nc2c(ncn2[C@H]2O[C@@H](COP(=O)(O)O)[C@@H](O)…`
ZINC3869963	1.000	363.2 Da LogP -2.57 TPSA 206.0	1 viol.	✓ Clean	`Nc1nc2c(ncn2[C@H]2O[C@@H](COP(=O)(O)O)[C@@H](O)…`
ZINC3869965	1.000	363.2 Da LogP -2.57 TPSA 206.0	1 viol.	✓ Clean	`Nc1nc2c(ncn2[C@@H]2O[C@@H](COP(=O)(O)O)[C@@H](O…`
ZINC4521877	1.000	234.3 Da LogP 1.61 TPSA 47.9	✓ Ro5	✓ Clean	`CCCCCCOCCOCCOCCO`
ZINC5273610	1.000	322.4 Da LogP 1.64 TPSA 66.4	✓ Ro5	✓ Clean	`CCCCCCOCCOCCOCCOCCOCCO`
ZINC58538366	1.000	392.6 Da LogP 3.59 TPSA 66.4	✓ Ro5	✓ Clean	`CCCCCCCCCCCOCCOCCOCCOCCOCCO`
ZINC58631420	1.000	422.6 Da LogP 3.22 TPSA 75.6	✓ Ro5	✓ Clean	`CCCCCCCCCCOCCOCCOCCOCCOCCOCCO`
ZINC59441819	1.000	318.5 Da LogP 3.95 TPSA 47.9	✓ Ro5	✓ Clean	`CCCCCCCCCCCCOCCOCCOCCO`
ZINC59622400	1.000	274.4 Da LogP 3.93 TPSA 38.7	✓ Ro5	✓ Clean	`CCCCCCCCCCCCOCCOCCO`
ZINC71788551	1.000	334.5 Da LogP 3.19 TPSA 57.2	✓ Ro5	✓ Clean	`CCCCCCCCCCOCCOCCOCCOCCO`
ZINC71788564	1.000	262.4 Da LogP 2.39 TPSA 47.9	✓ Ro5	✓ Clean	`CCCCCCCCOCCOCCOCCO`
ZINC71788567	1.000	406.6 Da LogP 3.98 TPSA 66.4	✓ Ro5	✓ Clean	`CCCCCCCCCCCCOCCOCCOCCOCCOCCO`
ZINC8214594	1.000	362.6 Da LogP 3.97 TPSA 57.2	✓ Ro5	✓ Clean	`CCCCCCCCCCCCOCCOCCOCCOCCO`
ZINC88260008	1.000	390.6 Da LogP 4.75 TPSA 57.2	✓ Ro5	✓ Clean	`CCCCCCCCCCCCCCOCCOCCOCCOCCO`
ZINC9334496	1.000	363.2 Da LogP -2.57 TPSA 206.0	1 viol.	✓ Clean	`Nc1nc2c(ncn2[C@H]2O[C@@H](COP(=O)(O)O)[C@H](O)[…`
ZINC95784968	1.000	450.7 Da LogP 4.00 TPSA 75.6	✓ Ro5	✓ Clean	`CCCCCCCCCCCCOCCOCCOCCOCCOCCOCCO`
ZINC95863931	1.000	464.7 Da LogP 4.39 TPSA 75.6	✓ Ro5	✓ Clean	`CCCCCCCCCCCCCOCCOCCOCCOCCOCCOCCO`
ZINC1849711	0.950	202.3 Da LogP 3.14 TPSA 29.5	✓ Ro5	✓ Clean	`CCCCCCCCCCOCCO`
ZINC1850542	0.950	216.4 Da LogP 3.53 TPSA 29.5	✓ Ro5	✓ Clean	`CCCCCCCCCCCOCCO`
ZINC2555269	0.950	220.3 Da LogP 1.22 TPSA 47.9	✓ Ro5	✓ Clean	`CCCCCOCCOCCOCCO`
ZINC59660505	0.950	244.4 Da LogP 4.31 TPSA 29.5	✓ Ro5	✓ Clean	`CCCCCCCCCCCCCOCCO`
ZINC8437287	0.950	230.4 Da LogP 3.92 TPSA 29.5	✓ Ro5	✓ Clean	`CCCCCCCCCCCCOCCO`
ZINC85733754	0.950	258.4 Da LogP 4.70 TPSA 29.5	✓ Ro5	✓ Clean	`CCCCCCCCCCCCCCOCCO`
ZINC3055005	0.882	204.2 Da LogP -0.63 TPSA 126.6	✓ Ro5	✓ Clean	`N[C@@H](CCCC[C@H](N)C(=O)O)C(=O)O`
ZINC3055007	0.882	204.2 Da LogP -0.63 TPSA 126.6	✓ Ro5	✓ Clean	`N[C@@H](CCCC[C@@H](N)C(=O)O)C(=O)O`
ZINC3055010	0.882	204.2 Da LogP -0.63 TPSA 126.6	✓ Ro5	✓ Clean	`N[C@H](CCCC[C@@H](N)C(=O)O)C(=O)O`
ZINC104869865	0.857	443.2 Da LogP -2.45 TPSA 252.6	2 viol.	✓ Clean	`Nc1nc2c(ncn2[C@H]2O[C@H](CO[P@@](=O)(O)OP(=O)(O…`
ZINC12504289	0.857	443.2 Da LogP -2.45 TPSA 252.6	2 viol.	✓ Clean	`Nc1nc2c(ncn2[C@@H]2O[C@H](CO[P@@](=O)(O)OP(=O)(…`
ZINC34541308	0.857	443.2 Da LogP -2.45 TPSA 252.6	2 viol.	✓ Clean	`Nc1nc2c(ncn2[C@@H]2O[C@H](CO[P@@](=O)(O)OP(=O)(…`
ZINC35000839	0.857	443.2 Da LogP -2.45 TPSA 252.6	2 viol.	✓ Clean	`Nc1nc2c(ncn2[C@H]2O[C@@H](CO[P@@](=O)(O)OP(=O)(…`
ZINC45284491	0.857	443.2 Da LogP -2.45 TPSA 252.6	2 viol.	✓ Clean	`Nc1nc2c(ncn2[C@H]2O[C@@H](CO[P@@](=O)(O)OP(=O)(…`
ZINC80639694	0.857	443.2 Da LogP -2.45 TPSA 252.6	2 viol.	✓ Clean	`Nc1nc2c(ncn2[C@@H]2O[C@H](CO[P@@](=O)(O)OP(=O)(…`
ZINC8215481	0.857	443.2 Da LogP -2.45 TPSA 252.6	2 viol.	✓ Clean	`Nc1nc2c(ncn2[C@@H]2O[C@H](CO[P@@](=O)(O)OP(=O)(…`
ZINC1720127	0.833	218.3 Da LogP -0.24 TPSA 126.6	✓ Ro5	✓ Clean	`N[C@@H](CCCCC[C@H](N)C(=O)O)C(=O)O`
ZINC1720128	0.833	218.3 Da LogP -0.24 TPSA 126.6	✓ Ro5	✓ Clean	`N[C@@H](CCCCC[C@@H](N)C(=O)O)C(=O)O`

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.