Protein profile

KP13_00647

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

Genome: KpKP13

Gene: AHE42267.1 ugpB Structure source: AlphaFold + ColabFold UniProt A0A0H3H458

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Amino acids 438

Annotations 1

Features 17

PDB binders 10

Druggability 0.425

Overview

Basic information about this protein and its source genome.

Accession: KP13_00647
Assembly: Klebsiella pneumoniae subsp. pneumoniae Kp13, complete sequence
Gene: AHE42267.1 ugpB
Status: annotated
Amino acids: 438
Structure source: AlphaFold + ColabFold

GO:0055085 The process in which a solute is transported across a lipid bilayer, from one side of a membrane to the other.

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: 94.69

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 0.425

Structure A0A0H3H458

Pocket Pocket 5

P2Rank 0.907

Structure A0A0H3H458

Pocket Pocket 1

ColabFold model

FPocket 0.781 · Pocket 2

P2Rank 0.902 · Pocket 1

Core conservation Conserved core gene

Roary core

CoreCruncher core

Gut microbiome 123 / 4744 genomes with a hit

Normalized 0.026

Sequence

Primary amino-acid sequence viewer.

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 GO

Gene Ontology (GO)

GO:0055085 The process in which a solute is transported across a lipid bilayer, from one side of a membrane to the other.

Sequence Features

Domain/signature hits from InterPro and related databases.

17 records

Show feature table

Start	End	DB	Term	Name
25	425	SUPERFAMILY	SSF53850	Periplasmic binding protein-like II
26	424	CDD	cd14748	PBP2_UgpB
1	23	Phobius	SIGNAL_PEPTIDE	Signal peptide region
1	23	SignalP_EUK	SignalP-noTM	SignalP-noTM
5	392	PANTHER	PTHR43649	ARABINOSE-BINDING PROTEIN-RELATED
145	424	Gene3D	G3DSA:3.40.190.10	-
1	6	Phobius	SIGNAL_PEPTIDE_N_REGION	N-terminal region of a signal peptide.
24	438	Phobius	NON_CYTOPLASMIC_DOMAIN	Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
7	18	Phobius	SIGNAL_PEPTIDE_H_REGION	Hydrophobic region of a signal peptide.
7	29	TMHMM	TMhelix	Region of a membrane-bound protein predicted to be embedded in the membrane.
29	383	Gene3D	G3DSA:3.40.190.10	-
140	157	ProSitePatterns	PS01037	Bacterial extracellular solute-binding proteins, family 1 signature.
140	157	InterPro	IPR006061	Solute-binding family 1, conserved site
1	23	SignalP_GRAM_POSITIVE	SignalP-TM	SignalP-TM
19	23	Phobius	SIGNAL_PEPTIDE_C_REGION	C-terminal region of a signal peptide.
44	366	Pfam	PF13416	Bacterial extracellular solute-binding protein
44	366	InterPro	IPR006059	Bacterial extracellular solute-binding protein

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_A0A0H3H458	AlphaFold	—	—	full sequence	—	Viewing
ColabFold KP13_00647	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
5				0.425
1				0.407
9				0.332

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	19.48	0.84
2	1.75	0.032
3	1.73	0.031
4	1.56	0.024
5	1.47	0.02

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				0.781
4				0.51
3				0.243

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	19.78	0.845
2	2.09	0.047
3	1.12	0.008
4	0.92	0.004
5	0.88	0.004

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.

60 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
BGQ	7C63	Q53W80	105.1 Da LogP -0.84 TPSA 60.4	✓ Ro5	✓ Clean	`C(CO)[C@H](C[O])O`
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	7C64	Q53W80	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`
MRY	7C64	Q53W80	122.1 Da LogP -2.31 TPSA 80.9	✓ Ro5	✓ Clean	`C([C@H]([C@H](CO)O)O)O`
P33	7C64	Q53W80	326.4 Da LogP -0.93 TPSA 95.8	✓ Ro5	✓ Clean	`C(COCCOCCOCCOCCOCCOCCO)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-]`
SO2	7C6Z	Q53W80	64.1 Da LogP -0.67 TPSA 34.1	✓ Ro5	✓ Clean	`O=S=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
ZINC12501520	1.000	458.5 Da LogP -0.88 TPSA 123.5	1 viol.	✓ Clean	`OCCOCCOCCOCCOCCOCCOCCOCCOCCOCCO`
ZINC3874716	1.000	414.5 Da LogP -0.90 TPSA 114.3	✓ Ro5	✓ Clean	`OCCOCCOCCOCCOCCOCCOCCOCCOCCO`
ZINC4283769	1.000	238.3 Da LogP -0.96 TPSA 77.4	✓ Ro5	✓ Clean	`OCCOCCOCCOCCOCCO`
ZINC4521548	1.000	282.3 Da LogP -0.95 TPSA 86.6	✓ Ro5	✓ Clean	`OCCOCCOCCOCCOCCOCCO`
ZINC5178829	1.000	326.4 Da LogP -0.93 TPSA 95.8	✓ Ro5	✓ Clean	`OCCOCCOCCOCCOCCOCCOCCO`
ZINC5178830	1.000	370.4 Da LogP -0.91 TPSA 105.1	✓ Ro5	✓ Clean	`OCCOCCOCCOCCOCCOCCOCCOCCO`
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`
ZINC115086873	0.688	209.2 Da LogP -1.08 TPSA 83.2	✓ Ro5	✓ Clean	`NOCCOCCOCCOCCO`
ZINC137432264	0.688	457.6 Da LogP -0.91 TPSA 129.3	1 viol.	✓ Clean	`NCCOCCOCCOCCOCCOCCOCCOCCOCCOCCO`
ZINC146143823	0.688	237.3 Da LogP -1.00 TPSA 83.2	✓ Ro5	✓ Clean	`NCCOCCOCCOCCOCCO`
ZINC1542984442	0.688	413.5 Da LogP -0.93 TPSA 120.1	✓ Ro5	✓ Clean	`NCCOCCOCCOCCOCCOCCOCCOCCOCCO`
ZINC1565503710	0.688	254.3 Da LogP -0.03 TPSA 57.2	✓ Ro5	✓ Clean	`OCCOCCOCCOCCOCCS`
ZINC1580161	0.688	208.3 Da LogP -0.33 TPSA 57.2	✓ Ro5	✓ Clean	`COCCOCCOCCOCCO`
ZINC16052118	0.688	340.4 Da LogP -0.28 TPSA 84.8	✓ Ro5	✓ Clean	`COCCOCCOCCOCCOCCOCCOCCO`
ZINC16052257	0.688	384.5 Da LogP -0.26 TPSA 94.1	✓ Ro5	✓ Clean	`COCCOCCOCCOCCOCCOCCOCCOCCO`
ZINC1857792028	0.688	430.6 Da LogP 0.04 TPSA 94.1	✓ Ro5	✓ Clean	`OCCOCCOCCOCCOCCOCCOCCOCCOCCS`
ZINC1857792057	0.688	474.6 Da LogP 0.06 TPSA 103.3	1 viol.	✓ Clean	`OCCOCCOCCOCCOCCOCCOCCOCCOCCOCCS`
ZINC230494776	0.688	325.4 Da LogP -0.96 TPSA 101.6	✓ Ro5	✓ Clean	`NCCOCCOCCOCCOCCOCCOCCO`
ZINC34317654	0.688	472.6 Da LogP -0.23 TPSA 112.5	1 viol.	✓ Clean	`COCCOCCOCCOCCOCCOCCOCCOCCOCCOCCO`
ZINC38917157	0.688	210.3 Da LogP -0.04 TPSA 47.9	✓ Ro5	✓ Clean	`OCCOCCOCCOCCS`
ZINC44076059	0.688	428.5 Da LogP -0.24 TPSA 103.3	✓ Ro5	✓ Clean	`COCCOCCOCCOCCOCCOCCOCCOCCOCCO`
ZINC5210101	0.688	252.3 Da LogP -0.31 TPSA 66.4	✓ Ro5	✓ Clean	`COCCOCCOCCOCCOCCO`
ZINC5650743	0.688	222.3 Da LogP 0.07 TPSA 57.2	✓ Ro5	✓ Clean	`CCOCCOCCOCCOCCO`
ZINC5997860	0.688	296.4 Da LogP -0.29 TPSA 75.6	✓ Ro5	✓ Clean	`COCCOCCOCCOCCOCCOCCO`
ZINC6403917	0.688	354.4 Da LogP 0.11 TPSA 84.8	✓ Ro5	✓ Clean	`CCOCCOCCOCCOCCOCCOCCOCCO`
ZINC77271182	0.688	281.3 Da LogP -0.98 TPSA 92.4	✓ Ro5	✓ Clean	`NCCOCCOCCOCCOCCOCCO`
ZINC83253921	0.688	369.5 Da LogP -0.95 TPSA 110.9	✓ Ro5	✓ Clean	`NCCOCCOCCOCCOCCOCCOCCOCCO`
ZINC90741446	0.688	386.5 Da LogP 0.02 TPSA 84.8	✓ Ro5	✓ Clean	`OCCOCCOCCOCCOCCOCCOCCOCCS`
ZINC90741447	0.688	298.4 Da LogP -0.01 TPSA 66.4	✓ Ro5	✓ Clean	`OCCOCCOCCOCCOCCOCCS`
ZINC144169243	0.647	281.3 Da LogP -1.37 TPSA 89.4	✓ Ro5	✓ Clean	`OCCOCCOCCNCCOCCOCCO`
ZINC205758716	0.647	457.6 Da LogP -1.31 TPSA 126.3	1 viol.	✓ Clean	`OCCOCCOCCOCCOCCNCCOCCOCCOCCOCCO`
ZINC575441396	0.647	369.5 Da LogP -1.34 TPSA 107.9	✓ Ro5	✓ Clean	`OCCOCCOCCOCCNCCOCCOCCOCCO`
ZINC5975509	0.640	202.1 Da LogP -2.19 TPSA 127.5	✓ Ro5	✓ Clean	`O=P(O)(O)OC[C@H](O)[C@H](O)CO`
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…`
ZINC100055463	0.615	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	0.615	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	0.615	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	0.615	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	0.615	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]…`
ZINC18120313	0.615	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	0.615	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`
ZINC4403105	0.615	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	0.615	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@…`

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.