Protein profile

KP13_01322

putative sn-glycerol-3-phosphate-binding periplasmic protein

Genome: KpKP13

Gene: AHE46613.1 Structure source: AlphaFold + ColabFold UniProt A0A0H3GHK7

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Amino acids 436

Annotations 1

Features 14

PDB binders 8

Druggability 0.896

Overview

Basic information about this protein and its source genome.

Accession: KP13_01322
Assembly: Klebsiella pneumoniae subsp. pneumoniae Kp13, complete sequence
Gene: AHE46613.1
Status: annotated
Amino acids: 436
Structure source: AlphaFold + ColabFold

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 (%): 0.0
Localization: Periplasmic
ColabFold pLDDT: 94.73

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 0.896

Structure A0A0H3GHK7

Pocket Pocket 1

P2Rank 0.739

Structure A0A0H3GHK7

Pocket Pocket 1

ColabFold model

FPocket 0.406 · Pocket 3

P2Rank 0.911 · Pocket 1

Core conservation Accessory gene

Roary core

CoreCruncher accessory

Gut microbiome 15 / 4744 genomes with a hit

Normalized 0.003

Sequence

Primary amino-acid sequence viewer.

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 GO

Gene Ontology (GO)

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.

14 records

Show feature table

Start	End	DB	Term	Name
45	360	Pfam	PF13416	Bacterial extracellular solute-binding protein
45	360	InterPro	IPR006059	Bacterial extracellular solute-binding protein
35	420	SUPERFAMILY	SSF53850	Periplasmic binding protein-like II
5	16	Phobius	SIGNAL_PEPTIDE_H_REGION	Hydrophobic region of a signal peptide.
35	381	Gene3D	G3DSA:3.40.190.10	-
14	421	PANTHER	PTHR43649	ARABINOSE-BINDING PROTEIN-RELATED
1	22	SignalP_GRAM_NEGATIVE	SignalP-noTM	SignalP-noTM
147	417	Gene3D	G3DSA:3.40.190.10	-
23	436	Phobius	NON_CYTOPLASMIC_DOMAIN	Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
1	22	SignalP_GRAM_POSITIVE	SignalP-TM	SignalP-TM
1	22	Phobius	SIGNAL_PEPTIDE	Signal peptide region
25	419	CDD	cd14748	PBP2_UgpB
17	22	Phobius	SIGNAL_PEPTIDE_C_REGION	C-terminal region of a signal peptide.
1	4	Phobius	SIGNAL_PEPTIDE_N_REGION	N-terminal region of a signal peptide.

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_A0A0H3GHK7	AlphaFold	—	—	full sequence	—	Viewing
ColabFold KP13_01322	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
1				0.896

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	12.79	0.662
2	2.23	0.054
3	1.39	0.017
4	0.65	0.001

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				0.406

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	24.46	0.899
2	1.87	0.037
3	1.4	0.018

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.

58 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
CH5	6R1B	P71619	258.2 Da LogP -0.82 TPSA 96.2	✓ Ro5	✓ Clean	`C[N+](C)(C)CCO[P@](=O)(O)OC[C@@H](CO)O`
CO2	7C0F	Q5SLB4	44.0 Da LogP -0.58 TPSA 34.1	✓ Ro5	✓ Clean	`C(=O)=O`
FGO	7C0F	Q5SLB4	629.5 Da LogP -3.39 TPSA 299.6	3 viol.	✓ Clean	`c1nc2c(n1[C@H]3[C@@H]4CC(C[C@@H]4[C@H](O3)COP(=…`
G3P	4AQ4	P0AG80	172.1 Da LogP -1.55 TPSA 107.2	✓ Ro5	✓ Clean	`C([C@H](COP(=O)(O)O)O)O`
MTL	4RYA	B9JRF8	182.2 Da LogP -3.59 TPSA 121.4	1 viol.	✓ Clean	`C([C@H]([C@H]([C@@H]([C@@H](CO)O)O)O)O)O`
PO2	7C0F	Q5SLB4	63.0 Da LogP -0.45 TPSA 40.1	✓ Ro5	✓ Clean	`[O-]P=O`
PO3	7C0K	Q5SLB4	79.0 Da LogP -1.64 TPSA 63.2	✓ Ro5	✓ Clean	`[O-][P-](=O)[O-]`
RB0	5IAI	B9JM84	152.1 Da LogP -2.95 TPSA 101.2	✓ Ro5	✓ Clean	`C([C@H](C([C@H](CO)O)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
ZINC100055463	0.917	212.2 Da LogP -4.22 TPSA 141.6	1 viol.	✓ Clean	`OC[C@H](O)[C@@H](O)[C@H](O)[C@H](O)[C@H](O)CO`
ZINC100064885	0.917	212.2 Da LogP -4.22 TPSA 141.6	1 viol.	✓ Clean	`OC[C@H](O)[C@@H](O)[C@@H](O)[C@H](O)[C@H](O)CO`
ZINC17780060	0.917	212.2 Da LogP -4.22 TPSA 141.6	1 viol.	✓ Clean	`OC[C@@H](O)[C@H](O)C(O)[C@H](O)[C@H](O)CO`
ZINC17952732	0.917	212.2 Da LogP -4.22 TPSA 141.6	1 viol.	✓ Clean	`OC[C@H](O)[C@@H](O)C(O)[C@H](O)[C@H](O)CO`
ZINC18120313	0.917	212.2 Da LogP -4.22 TPSA 141.6	1 viol.	✓ Clean	`OC[C@H](O)[C@H](O)C(O)[C@H](O)[C@H](O)CO`
ZINC3979006	0.917	212.2 Da LogP -4.22 TPSA 141.6	1 viol.	✓ Clean	`OC[C@@H](O)[C@@H](O)C(O)[C@H](O)[C@H](O)CO`
ZINC4403103	0.917	242.2 Da LogP -4.86 TPSA 161.8	1 viol.	✓ Clean	`OC[C@@H](O)[C@H](O)[C@H](O)[C@H](O)[C@H](O)[C@H…`
ZINC4403105	0.917	242.2 Da LogP -4.86 TPSA 161.8	1 viol.	✓ Clean	`OC[C@H](O)[C@@H](O)[C@H](O)[C@H](O)[C@H](O)[C@H…`
ZINC4403107	0.917	242.2 Da LogP -4.86 TPSA 161.8	1 viol.	✓ Clean	`OC[C@@H](O)[C@@H](O)[C@H](O)[C@H](O)[C@H](O)[C@…`
ZINC9212412	0.917	212.2 Da LogP -4.22 TPSA 141.6	1 viol.	✓ Clean	`OC[C@H](O)[C@@H](O)C(O)[C@H](O)[C@@H](O)CO`
ZINC18042331	0.769	242.2 Da LogP -4.86 TPSA 161.8	1 viol.	✓ Clean	`OC[C@H](O)[C@H](O)[C@H](O)[C@H](O)[C@H](O)[C@H]…`
ZINC1529618	0.739	246.2 Da LogP -2.17 TPSA 136.7	✓ Ro5	✓ Clean	`O=P(O)(OC[C@@H](O)CO)OC[C@H](O)CO`
ZINC1529620	0.739	246.2 Da LogP -2.17 TPSA 136.7	✓ Ro5	✓ Clean	`O=P(O)(OC[C@@H](O)CO)OC[C@@H](O)CO`
ZINC5201837	0.647	345.3 Da LogP -6.55 TPSA 214.3	2 viol.	✓ Clean	`OC[C@@H](O)[C@@H](O)[C@@H](O)[C@@H](O)CNC[C@H](…`
ZINC5201838	0.647	345.3 Da LogP -6.55 TPSA 214.3	2 viol.	✓ Clean	`OC[C@@H](O)[C@@H](O)[C@@H](O)[C@@H](O)CNC[C@@H]…`
ZINC5201839	0.647	345.3 Da LogP -6.55 TPSA 214.3	2 viol.	✓ Clean	`OC[C@@H](O)[C@@H](O)[C@@H](O)[C@@H](O)CNC[C@H](…`
ZINC5201841	0.647	345.3 Da LogP -6.55 TPSA 214.3	2 viol.	✓ Clean	`OC[C@@H](O)[C@@H](O)[C@@H](O)[C@@H](O)CNC[C@@H]…`
ZINC12503440	0.620	363.2 Da LogP -2.57 TPSA 206.0	1 viol.	✓ Clean	`Nc1nc2c(ncn2[C@@H]2O[C@H](CO)[C@@H](OP(=O)(O)O)…`
ZINC1530370	0.620	363.2 Da LogP -2.57 TPSA 206.0	1 viol.	✓ Clean	`Nc1nc2c(ncn2[C@H]2O[C@@H](CO)[C@H](OP(=O)(O)O)[…`
ZINC28631009	0.620	363.2 Da LogP -2.57 TPSA 206.0	1 viol.	✓ Clean	`Nc1nc2c(ncn2[C@@H]2O[C@H](CO)[C@H](OP(=O)(O)O)[…`
ZINC3872740	0.620	363.2 Da LogP -2.57 TPSA 206.0	1 viol.	✓ Clean	`Nc1nc2c(ncn2[C@H]2O[C@@H](CO)[C@@H](OP(=O)(O)O)…`
ZINC3872741	0.620	363.2 Da LogP -2.57 TPSA 206.0	1 viol.	✓ Clean	`Nc1nc2c(ncn2[C@@H]2O[C@@H](CO)[C@@H](OP(=O)(O)O…`
ZINC3872742	0.620	363.2 Da LogP -2.57 TPSA 206.0	1 viol.	✓ Clean	`Nc1nc2c(ncn2[C@H]2O[C@@H](CO)[C@@H](OP(=O)(O)O)…`
ZINC3872743	0.620	363.2 Da LogP -2.57 TPSA 206.0	1 viol.	✓ Clean	`Nc1nc2c(ncn2[C@@H]2O[C@@H](CO)[C@@H](OP(=O)(O)O…`
ZINC101356848	0.579	388.4 Da LogP -6.96 TPSA 226.4	2 viol.	✓ Clean	`OC[C@H](O)[C@H](O)[C@H](O)[C@H](O)CNCCNC[C@H](O…`
ZINC215968865	0.579	388.4 Da LogP -6.96 TPSA 226.4	2 viol.	✓ Clean	`OC[C@H](O)[C@H](O)[C@H](O)[C@H](O)CNCCNC[C@H](O…`
ZINC215968917	0.579	388.4 Da LogP -6.96 TPSA 226.4	2 viol.	✓ Clean	`OC[C@H](O)[C@H](O)[C@H](O)[C@H](O)CNCCNC[C@H](O…`
ZINC215968963	0.579	388.4 Da LogP -6.96 TPSA 226.4	2 viol.	✓ Clean	`OC[C@H](O)[C@H](O)[C@@H](O)[C@@H](O)CNCCNC[C@@H…`
ZINC216185927	0.579	209.2 Da LogP -3.02 TPSA 104.4	✓ Ro5	✓ Clean	`CN(C)C[C@H](O)[C@H](O)[C@H](O)[C@@H](O)CO`
ZINC216185976	0.579	209.2 Da LogP -3.02 TPSA 104.4	✓ Ro5	✓ Clean	`CN(C)C[C@H](O)[C@H](O)[C@@H](O)[C@H](O)CO`
ZINC216186168	0.579	224.3 Da LogP -2.87 TPSA 101.2	✓ Ro5	✓ Clean	`C[N+](C)(C)C[C@H](O)[C@H](O)[C@H](O)[C@@H](O)CO`
ZINC216186206	0.579	224.3 Da LogP -2.87 TPSA 101.2	✓ Ro5	✓ Clean	`C[N+](C)(C)C[C@H](O)[C@H](O)[C@@H](O)[C@H](O)CO`
ZINC25624721	0.579	209.2 Da LogP -3.02 TPSA 104.4	✓ Ro5	✓ Clean	`CN(C)C[C@H](O)[C@H](O)[C@@H](O)[C@@H](O)CO`
ZINC25624980	0.579	224.3 Da LogP -2.87 TPSA 101.2	✓ Ro5	✓ Clean	`C[N+](C)(C)C[C@H](O)[C@H](O)[C@@H](O)[C@@H](O)CO`
ZINC4566610	0.579	209.2 Da LogP -3.02 TPSA 104.4	✓ Ro5	✓ Clean	`CN(C)C[C@H](O)[C@H](O)[C@H](O)[C@H](O)CO`
ZINC4566614	0.579	224.3 Da LogP -2.87 TPSA 101.2	✓ Ro5	✓ Clean	`C[N+](C)(C)C[C@H](O)[C@H](O)[C@H](O)[C@H](O)CO`
ZINC13507210	0.578	356.4 Da LogP 1.31 TPSA 102.3	✓ Ro5	✓ Clean	`CCCCCC(=O)OC[C@@H](O)CO[P@](=O)(O)OCC[N+](C)(C)C`
ZINC1560408744	0.568	257.2 Da LogP -0.28 TPSA 96.2	✓ Ro5	✓ Clean	`C[N+](C)(C)CCO[P@](=O)(O)OC[C](O)CO`
ZINC4095590	0.567	215.1 Da LogP -1.57 TPSA 122.2	✓ Ro5	✓ Clean	`NCCO[P@@](=O)(O)OC[C@H](O)CO`
ZINC4095591	0.567	215.1 Da LogP -1.57 TPSA 122.2	✓ Ro5	✓ Clean	`NCCO[P@@](=O)(O)OC[C@@H](O)CO`
ZINC102189757	0.565	454.6 Da LogP 4.04 TPSA 102.3	✓ Ro5	✓ Clean	`CCCCCCCCCCCCC(=O)OC[C@H](O)CO[P@@](=O)(O)OCC[N+…`
ZINC14880038	0.565	440.5 Da LogP 3.65 TPSA 102.3	✓ Ro5	✓ Clean	`CCCCCCCCCCCC(=O)OC[C@@H](O)CO[P@](=O)(O)OCC[N+]…`
ZINC14880039	0.565	440.5 Da LogP 3.65 TPSA 102.3	✓ Ro5	✓ Clean	`CCCCCCCCCCCC(=O)OC[C@H](O)CO[P@@](=O)(O)OCC[N+]…`
ZINC15297567	0.565	468.6 Da LogP 4.43 TPSA 102.3	✓ Ro5	✓ Clean	`CCCCCCCCCCCCCC(=O)OC[C@@H](O)CO[P@@](=O)(O)OCC[…`
ZINC32789157	0.565	412.5 Da LogP 2.87 TPSA 102.3	✓ Ro5	✓ Clean	`CCCCCCCCCC(=O)OC[C@@H](O)CO[P@](=O)(O)OCC[N+](C…`
ZINC32822149	0.565	468.6 Da LogP 4.43 TPSA 102.3	✓ Ro5	✓ Clean	`CCCCCCCCCCCCCC(=O)OC[C@H](O)CO[P@](=O)(O)OCC[N+…`
ZINC32822162	0.565	482.6 Da LogP 4.82 TPSA 102.3	✓ Ro5	✓ Clean	`CCCCCCCCCCCCCCC(=O)OC[C@@H](O)CO[P@@](=O)(O)OCC…`
ZINC32822163	0.565	482.6 Da LogP 4.82 TPSA 102.3	✓ Ro5	✓ Clean	`CCCCCCCCCCCCCCC(=O)OC[C@H](O)CO[P@](=O)(O)OCC[N…`
ZINC44305349	0.565	454.6 Da LogP 4.04 TPSA 102.3	✓ Ro5	✓ Clean	`CCCCCCCCCCCCC(=O)OC[C@@H](O)CO[P@@](=O)(O)OCC[N…`
ZINC44405722	0.565	426.5 Da LogP 3.26 TPSA 102.3	✓ Ro5	✓ Clean	`CCCCCCCCCCC(=O)OC[C@@H](O)CO[P@@](=O)(O)OCC[N+]…`

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.