Protein profile

KP13_04834

Outer membrane protein S1

Genome: KpKP13

Gene: ompS1 AHE43801.1 Structure source: AlphaFold + ColabFold UniProt A0A0H3GVL2

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Amino acids 381

Annotations 5

Features 39

PDB binders 7

Druggability 0.99

Overview

Basic information about this protein and its source genome.

Accession: KP13_04834
Assembly: Klebsiella pneumoniae subsp. pneumoniae Kp13, complete sequence
Gene: ompS1 AHE43801.1
Status: annotated
Amino acids: 381
Structure source: AlphaFold + ColabFold

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:0016020 A lipid bilayer along with all the proteins and protein complexes embedded in it and attached to it. 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: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:0046930 A protein complex providing a discrete opening in a membrane that allows the passage of gases and/or liquids.

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 (%): 74.805
DEG E-value: 0.0
Localization: OuterMembrane
ColabFold pLDDT: 91.88

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 0.99

Structure A0A0H3GVL2

Pocket Pocket 7

P2Rank 0.732

Structure A0A0H3GVL2

Pocket Pocket 1

ColabFold model

FPocket 0.685 · Pocket 5

P2Rank 0.721 · Pocket 1

Core conservation Conserved core gene

Roary core

CoreCruncher core

Gut microbiome 112 / 4744 genomes with a hit

Normalized 0.024

Sequence

Primary amino-acid sequence viewer.

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

5 GO

Gene Ontology (GO)

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:0016020 A lipid bilayer along with all the proteins and protein complexes embedded in it and attached to it.
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: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:0046930 A protein complex providing a discrete opening in a membrane that allows the passage of gases and/or liquids.

Sequence Features

Domain/signature hits from InterPro and related databases.

39 records

Show feature table

Start	End	DB	Term	Name
30	381	CDD	cd00342	gram_neg_porins
30	381	InterPro	IPR033900	Porin domain, Gram-negative type
5	16	Phobius	SIGNAL_PEPTIDE_H_REGION	Hydrophobic region of a signal peptide.
22	38	PRINTS	PR00183	E.coli/Salmonella-type porin signature
22	38	InterPro	IPR001897	Porin, gammaproteobacterial
51	69	PRINTS	PR00183	E.coli/Salmonella-type porin signature
51	69	InterPro	IPR001897	Porin, gammaproteobacterial
282	301	PRINTS	PR00183	E.coli/Salmonella-type porin signature
282	301	InterPro	IPR001897	Porin, gammaproteobacterial
250	267	PRINTS	PR00183	E.coli/Salmonella-type porin signature
250	267	InterPro	IPR001897	Porin, gammaproteobacterial
95	117	PRINTS	PR00183	E.coli/Salmonella-type porin signature
95	117	InterPro	IPR001897	Porin, gammaproteobacterial
150	172	PRINTS	PR00183	E.coli/Salmonella-type porin signature
150	172	InterPro	IPR001897	Porin, gammaproteobacterial
1	21	SignalP_GRAM_NEGATIVE	SignalP-noTM	SignalP-noTM
1	381	PANTHER	PTHR34501	PROTEIN YDDL-RELATED
17	21	Phobius	SIGNAL_PEPTIDE_C_REGION	C-terminal region of a signal peptide.
22	381	SUPERFAMILY	SSF56935	Porins
22	381	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
1	21	SignalP_GRAM_POSITIVE	SignalP-TM	SignalP-TM
27	381	Pfam	PF00267	Gram-negative porin
27	381	InterPro	IPR001702	Porin, Gram-negative type
22	381	Gene3D	G3DSA:2.40.160.10	Porin
22	381	InterPro	IPR023614	Porin domain superfamily
332	348	ProSitePatterns	PS00576	General diffusion Gram-negative porins signature.
332	348	InterPro	IPR013793	Porin, Gram-negative type, conserved site
1	4	Phobius	SIGNAL_PEPTIDE_N_REGION	N-terminal region of a signal peptide.
332	349	PRINTS	PR00182	E.coli/Neisseria porin superfamily signature
332	349	InterPro	IPR001702	Porin, Gram-negative type
244	256	PRINTS	PR00182	E.coli/Neisseria porin superfamily signature
244	256	InterPro	IPR001702	Porin, Gram-negative type
52	63	PRINTS	PR00182	E.coli/Neisseria porin superfamily signature
52	63	InterPro	IPR001702	Porin, Gram-negative type
152	163	PRINTS	PR00182	E.coli/Neisseria porin superfamily signature
152	163	InterPro	IPR001702	Porin, Gram-negative type
95	105	PRINTS	PR00182	E.coli/Neisseria porin superfamily signature
95	105	InterPro	IPR001702	Porin, Gram-negative type

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_A0A0H3GVL2	AlphaFold	—	—	full sequence	—	Viewing
ColabFold KP13_04834	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
7				0.99

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	11.23	0.601
2	6.1	0.302
3	2.98	0.097
4	2.44	0.066
5	2.43	0.066

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				0.685

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	5.34	0.252
2	3.44	0.124
3	2.92	0.094
4	2.57	0.073
5	2.02	0.044

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.

57 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
C8E	5O79	D6QLY0	306.4 Da LogP 2.41 TPSA 57.2	✓ Ro5	✓ Clean	`CCCCCCCCOCCOCCOCCOCCO`
D10	2XE1	Q8CVW1	142.3 Da LogP 4.15 TPSA 0.0	✓ Ro5	✓ Clean	`CCCCCCCCCC`
D12	1OSM	Q48473	170.3 Da LogP 4.93 TPSA 0.0	✓ Ro5	✓ Clean	`CCCCCCCCCCCC`
HEX	2XE1	Q8CVW1	86.2 Da LogP 2.59 TPSA 0.0	✓ Ro5	✓ Clean	`CCCCCC`
LDA	6RCK	D6QLY1	229.4 Da LogP 4.48 TPSA 23.1	✓ Ro5	✓ Clean	`CCCCCCCCCCCC[N+](C)(C)[O-]`
LMT	5NUP	F2VN85	510.6 Da LogP -0.45 TPSA 178.5	3 viol.	✓ Clean	`CCCCCCCCCCCCO[C@H]1[C@@H]([C@H]([C@@H]([C@H](O1…`
P6L	6RCK	D6QLY1	747.0 Da LogP 10.22 TPSA 148.8	2 viol.	✓ Clean	`CCCCCCCCCC=CCCCCCCC(=O)OC[C@@H](CO[P@](=O)(O)OC…`

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
ZINC100053689	1.000	482.6 Da LogP -1.23 TPSA 178.5	2 viol.	✓ Clean	`CCCCCCCCCCO[C@H]1O[C@H](CO)[C@@H](O[C@H]2O[C@H]…`
ZINC100053691	1.000	496.6 Da LogP -0.84 TPSA 178.5	2 viol.	✓ Clean	`CCCCCCCCCCCO[C@H]1O[C@H](CO)[C@@H](O[C@H]2O[C@H…`
ZINC1501015302	1.000	482.6 Da LogP -1.23 TPSA 178.5	2 viol.	✓ Clean	`CCCCCCCCCCO[C@@H]1O[C@H](CO)[C@@H](O[C@H]2O[C@H…`
ZINC2039285652	1.000	454.5 Da LogP -2.01 TPSA 178.5	2 viol.	✓ Clean	`CCCCCCCCO[C@H]1O[C@H](CO)[C@H](O[C@@H]2O[C@H](C…`
ZINC2039285653	1.000	454.5 Da LogP -2.01 TPSA 178.5	2 viol.	✓ Clean	`CCCCCCCCO[C@H]1O[C@H](CO)[C@H](O[C@@H]2O[C@H](C…`
ZINC2039285654	1.000	454.5 Da LogP -2.01 TPSA 178.5	2 viol.	✓ Clean	`CCCCCCCCO[C@H]1O[C@H](CO)[C@H](O[C@@H]2O[C@H](C…`
ZINC2039285655	1.000	454.5 Da LogP -2.01 TPSA 178.5	2 viol.	✓ Clean	`CCCCCCCCO[C@H]1O[C@H](CO)[C@H](O[C@@H]2O[C@H](C…`
ZINC2053493146	1.000	482.6 Da LogP -1.23 TPSA 178.5	2 viol.	✓ Clean	`CCCCCCCCCCO[C@H]1O[C@H](CO)[C@H](O[C@@H]2O[C@H]…`
ZINC2053493147	1.000	482.6 Da LogP -1.23 TPSA 178.5	2 viol.	✓ Clean	`CCCCCCCCCCO[C@H]1O[C@H](CO)[C@H](O[C@@H]2O[C@H]…`
ZINC2053493148	1.000	482.6 Da LogP -1.23 TPSA 178.5	2 viol.	✓ Clean	`CCCCCCCCCCO[C@H]1O[C@H](CO)[C@H](O[C@@H]2O[C@H]…`
ZINC2053493149	1.000	482.6 Da LogP -1.23 TPSA 178.5	2 viol.	✓ Clean	`CCCCCCCCCCO[C@H]1O[C@H](CO)[C@H](O[C@@H]2O[C@H]…`
ZINC238809244	1.000	510.6 Da LogP -0.45 TPSA 178.5	3 viol.	✓ Clean	`CCCCCCCCCCCCO[C@@H]1O[C@H](CO)[C@@H](O[C@H]2O[C…`
ZINC238809245	1.000	510.6 Da LogP -0.45 TPSA 178.5	3 viol.	✓ Clean	`CCCCCCCCCCCCO[C@@H]1O[C@H](CO)[C@@H](O[C@H]2O[C…`
ZINC252695223	1.000	482.6 Da LogP -1.23 TPSA 178.5	2 viol.	✓ Clean	`CCCCCCCCCCO[C@@H]1O[C@H](CO)[C@@H](O[C@H]2O[C@H…`
ZINC252695224	1.000	482.6 Da LogP -1.23 TPSA 178.5	2 viol.	✓ Clean	`CCCCCCCCCCO[C@@H]1O[C@H](CO)[C@@H](O[C@H]2O[C@H…`
ZINC252695225	1.000	482.6 Da LogP -1.23 TPSA 178.5	2 viol.	✓ Clean	`CCCCCCCCCCO[C@@H]1O[C@H](CO)[C@@H](O[C@H]2O[C@H…`
ZINC252695226	1.000	482.6 Da LogP -1.23 TPSA 178.5	2 viol.	✓ Clean	`CCCCCCCCCCO[C@@H]1O[C@H](CO)[C@@H](O[C@H]2O[C@H…`
ZINC2584424	1.000	218.3 Da LogP 2.37 TPSA 38.7	✓ Ro5	✓ Clean	`CCCCCCCCOCCOCCO`
ZINC58649715	1.000	496.6 Da LogP -0.84 TPSA 178.5	2 viol.	✓ Clean	`CCCCCCCCCCCO[C@@H]1O[C@H](CO)[C@@H](O[C@H]2O[C@…`
ZINC59978443	1.000	454.5 Da LogP -2.01 TPSA 178.5	2 viol.	✓ Clean	`CCCCCCCCO[C@@H]1O[C@H](CO)[C@@H](O[C@H]2O[C@H](…`
ZINC66157001	1.000	468.5 Da LogP -1.62 TPSA 178.5	2 viol.	✓ Clean	`CCCCCCCCCO[C@@H]1O[C@H](CO)[C@@H](O[C@H]2O[C@H]…`
ZINC70669940	1.000	482.6 Da LogP -1.23 TPSA 178.5	2 viol.	✓ Clean	`CCCCCCCCCCO[C@@H]1O[C@@H](CO)[C@@H](O[C@H]2O[C@…`
ZINC70669941	1.000	482.6 Da LogP -1.23 TPSA 178.5	2 viol.	✓ Clean	`CCCCCCCCCCO[C@@H]1O[C@@H](CO)[C@@H](O[C@H]2O[C@…`
ZINC70669942	1.000	482.6 Da LogP -1.23 TPSA 178.5	2 viol.	✓ Clean	`CCCCCCCCCCO[C@@H]1O[C@@H](CO)[C@@H](O[C@H]2O[C@…`
ZINC70669943	1.000	482.6 Da LogP -1.23 TPSA 178.5	2 viol.	✓ Clean	`CCCCCCCCCCO[C@@H]1O[C@@H](CO)[C@@H](O[C@H]2O[C@…`
ZINC77311968	1.000	454.5 Da LogP -2.01 TPSA 178.5	2 viol.	✓ Clean	`CCCCCCCCO[C@@H]1O[C@H](CO)[C@@H](O[C@@H]2O[C@H]…`
ZINC83433913	1.000	426.5 Da LogP -2.79 TPSA 178.5	2 viol.	✓ Clean	`CCCCCCO[C@@H]1O[C@H](CO)[C@@H](O[C@H]2O[C@H](CO…`
ZINC85482724	1.000	482.6 Da LogP -1.23 TPSA 178.5	2 viol.	✓ Clean	`CCCCCCCCCCO[C@@H]1O[C@H](CO)[C@@H](O[C@H]2O[C@H…`
ZINC86002923	1.000	426.5 Da LogP -2.79 TPSA 178.5	2 viol.	✓ Clean	`CCCCCCO[C@@H]1O[C@H](CO)[C@H](O[C@H]2O[C@H](CO)…`
ZINC102191119	0.875	498.6 Da LogP 3.65 TPSA 148.8	✓ Ro5	✓ Clean	`CCCCCCCC(=O)OC[C@H](CO[P@@](=O)(O)OC[C@@H](O)CO…`
ZINC58649551	0.875	498.6 Da LogP 3.65 TPSA 148.8	✓ Ro5	✓ Clean	`CCCCCCCC(=O)OC[C@H](CO[P@@](=O)(O)OC[C@H](O)CO)…`
ZINC1644613	0.810	206.3 Da LogP 0.83 TPSA 47.9	✓ Ro5	✓ Clean	`CCCCOCCOCCOCCO`
ZINC38308095	0.795	384.4 Da LogP -3.96 TPSA 178.5	2 viol.	✓ Clean	`CCCO[C@@H]1O[C@H](CO)[C@@H](O[C@@H]2O[C@H](CO)[…`
ZINC13515170	0.711	236.3 Da LogP -1.40 TPSA 99.4	✓ Ro5	✓ Clean	`CCCCO[C@H]1O[C@H](CO)[C@@H](O)[C@H](O)[C@H]1O`
ZINC5821543	0.711	236.3 Da LogP -1.40 TPSA 99.4	✓ Ro5	✓ Clean	`CCCCO[C@@H]1O[C@H](CO)[C@@H](O)[C@H](O)[C@H]1O`
ZINC102191158	0.700	456.5 Da LogP 3.08 TPSA 142.8	✓ Ro5	✓ Clean	`CCCCCCCCCCCCCC(=O)OC[C@H](O)CO[P@@](=O)(O)OC[C@…`
ZINC14880758	0.700	484.6 Da LogP 3.86 TPSA 142.8	✓ Ro5	✓ Clean	`CCCCCCCCCCCCCCCC(=O)OC[C@@H](O)CO[P@](=O)(O)OC[…`
ZINC14880760	0.700	484.6 Da LogP 3.86 TPSA 142.8	✓ Ro5	✓ Clean	`CCCCCCCCCCCCCCCC(=O)OC[C@H](O)CO[P@](=O)(O)OC[C…`
ZINC53683910	0.700	484.6 Da LogP 3.86 TPSA 142.8	✓ Ro5	✓ Clean	`CCCCCCCCCCCCCCCC(=O)OC[C@H](O)CO[P@@](=O)(O)OC[…`
ZINC62592202	0.700	456.5 Da LogP 3.08 TPSA 142.8	✓ Ro5	✓ Clean	`CCCCCCCCCCCCCC(=O)OC[C@H](O)CO[P@@](=O)(O)OC[C@…`
ZINC62592203	0.700	456.5 Da LogP 3.08 TPSA 142.8	✓ Ro5	✓ Clean	`CCCCCCCCCCCCCC(=O)OC[C@@H](O)CO[P@@](=O)(O)OC[C…`
ZINC62592204	0.700	484.6 Da LogP 3.86 TPSA 142.8	✓ Ro5	✓ Clean	`CCCCCCCCCCCCCCCC(=O)OC[C@@H](O)CO[P@@](=O)(O)OC…`
ZINC96094841	0.700	456.5 Da LogP 3.08 TPSA 142.8	✓ Ro5	✓ Clean	`CCCCCCCCCCCCCC(=O)OC[C@@H](O)CO[P@@](=O)(O)OC[C…`
ZINC100053481	0.696	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	0.696	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	0.696	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	0.696	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	0.696	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…`
ZINC2386335433	0.696	467.5 Da LogP -2.50 TPSA 227.3	2 viol.	Alert	`[N-]=[N+]=NCCCCCCO[C@@H]1O[C@H](CO)[C@@H](O[C@@…`
ZINC14881288	0.681	494.6 Da LogP -1.23 TPSA 178.5	2 viol.	✓ Clean	`OC[C@H]1O[C@H](O[C@@H]2[C@@H](CO)O[C@@H](OCCCCC…`

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.