Protein profile

VK055_1926

periplasmic binding family protein

Genome: KpATCC43816

Gene: AIK80532.1 fepB Structure source: AlphaFold + ColabFold UniProt A0A0H3GL81

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Amino acids 319

Annotations 2

Features 19

PDB binders 11

Druggability 0.382

Overview

Basic information about this protein and its source genome.

Accession: VK055_1926
Assembly: Klebsiella pneumoniae subsp. pneumoniae strain ATCC 43816 KPPR1, complete genome
Gene: AIK80532.1 fepB
Status: annotated
Amino acids: 319
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. GO:1901678 The directed movement of an iron coordination entity into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.

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 (%): 84.615
DEG E-value: 0.0
Localization: Periplasmic
ColabFold pLDDT: 91.37

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 0.382

Structure A0A0H3GL81

Pocket Pocket 1

P2Rank 0.069

Structure A0A0H3GL81

Pocket Pocket 1

ColabFold model

FPocket 0.479 · Pocket 8

P2Rank 0.202 · Pocket 1

Core conservation Conserved core gene

Roary core

CoreCruncher core

Gut microbiome 81 / 4744 genomes with a hit

Normalized 0.017

Sequence

Primary amino-acid sequence viewer.

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

2 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.
GO:1901678 The directed movement of an iron coordination entity into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.

Sequence Features

Domain/signature hits from InterPro and related databases.

19 records

Show feature table

Start	End	DB	Term	Name
1	26	SignalP_EUK	SignalP-noTM	SignalP-noTM
146	318	FunFam	G3DSA:3.40.50.1980:FF:000014	Ferrienterobactin-binding periplasmic protein FepB
27	319	Phobius	NON_CYTOPLASMIC_DOMAIN	Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
1	26	SignalP_GRAM_POSITIVE	SignalP-TM	SignalP-TM
166	186	Coils	Coil	Coil
27	145	FunFam	G3DSA:3.40.50.1980:FF:000009	Iron-enterobactin transporter periplasmic binding protein
27	145	Gene3D	G3DSA:3.40.50.1980	Nitrogenase molybdenum iron protein domain
1	9	Phobius	SIGNAL_PEPTIDE_N_REGION	N-terminal region of a signal peptide.
48	319	ProSiteProfiles	PS50983	Iron siderophore/cobalamin periplasmic-binding domain profile.
48	319	InterPro	IPR002491	ABC transporter periplasmic binding domain
44	313	CDD	cd01146	FhuD
22	26	Phobius	SIGNAL_PEPTIDE_C_REGION	C-terminal region of a signal peptide.
49	296	Pfam	PF01497	Periplasmic binding protein
49	296	InterPro	IPR002491	ABC transporter periplasmic binding domain
31	315	SUPERFAMILY	SSF53807	Helical backbone metal receptor
1	26	Phobius	SIGNAL_PEPTIDE	Signal peptide region
10	21	Phobius	SIGNAL_PEPTIDE_H_REGION	Hydrophobic region of a signal peptide.
17	314	PANTHER	PTHR30532	IRON III DICITRATE-BINDING PERIPLASMIC PROTEIN
146	319	Gene3D	G3DSA:3.40.50.1980	Nitrogenase molybdenum iron protein 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

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_A0A0H3GL81	AlphaFold	—	—	full sequence	—	Viewing
ColabFold VK055_1926	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				0.382
6				0.003
8				0.002
14				0.001

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				2.79	0.069
2				2.77	0.068

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
8				0.479
1				0.268
3				0.002
4				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	Sticks	Spheres	Surfaces	Score	Probability	Labels	Zoom	Positions
1				5.25	0.202
2				0.75	0.002

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.

61 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
5LC	5A5D	Q0P8Q4	374.4 Da LogP 1.84 TPSA 139.1	1 viol.	Alert	`c1cc(c(c(c1)O)O)C(=O)NCCCCCNC(=O)c2cccc(c2O)O`
7PG	5FLY	A0A2P5JFB2	384.5 Da LogP -0.26 TPSA 94.1	✓ Ro5	✓ Clean	`COCCOCCOCCOCCOCCOCCOCCOCCO`
8LC	5AD1	Q0P8Q4	416.5 Da LogP 3.01 TPSA 139.1	1 viol.	Alert	`c1cc(c(c(c1)O)O)C(=O)NCCCCCCCCNC(=O)c2cccc(c2O)O`
95B	5OAH	Q0P8Q4	418.4 Da LogP 1.29 TPSA 176.4	1 viol.	Alert	`c1cc(c(c(c1)O)O)C(=O)NCCCC[C@@H](C(=O)O)NC(=O)c…`
9RT	5OD5	Q0P8Q4	277.3 Da LogP 1.02 TPSA 85.1	✓ Ro5	✓ Clean	`c1ccnc(c1)CNS(=O)(=O)c2ccc(cc2)CN`
DBS	5ADV	Q0P8Q4	241.2 Da LogP -0.73 TPSA 127.1	✓ Ro5	Alert	`c1cc(c(c(c1)O)O)C(=O)N[C@@H](CO)C(=O)O`
EB4	3TLK	P0AEL6	669.6 Da LogP -0.74 TPSA 287.6	3 viol.	Alert	`c1cc(c(c(c1)O)O)C(=O)N[C@H]2COC(=O)[C@H](COC(=O…`
EHS	5ADV	Q0P8Q4	464.4 Da LogP -0.97 TPSA 222.9	1 viol.	Alert	`c1cc(c(c(c1)O)O)C(=O)N[C@@H](CO)C(=O)OC[C@@H](C…`
LCM	5A1J	Q0P8Q4	360.4 Da LogP 1.45 TPSA 139.1	1 viol.	Alert	`c1cc(c(c(c1)O)O)C(=O)NCCCCNC(=O)c2cccc(c2O)O`
PXJ	5A5V	Q0P8Q4	388.4 Da LogP 2.23 TPSA 139.1	1 viol.	Alert	`c1cc(c(c(c1)O)O)C(=O)NCCCCCCNC(=O)c2cccc(c2O)O`
VBN	3R5T	Q9RCF6	705.7 Da LogP 1.84 TPSA 243.1	3 viol.	Alert	`C[C@@H]1[C@H](N=C(O1)c2cccc(c2O)O)C(=O)NCCCN(CC…`

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
ZINC142623932	1.000	464.4 Da LogP -0.97 TPSA 222.9	1 viol.	Alert	`O=C(N[C@@H](COC(=O)[C@H](CO)NC(=O)c1cccc(O)c1O)…`
ZINC1580161	1.000	208.3 Da LogP -0.33 TPSA 57.2	✓ Ro5	✓ Clean	`COCCOCCOCCOCCO`
ZINC16052118	1.000	340.4 Da LogP -0.28 TPSA 84.8	✓ Ro5	✓ Clean	`COCCOCCOCCOCCOCCOCCOCCO`
ZINC16052257	1.000	384.5 Da LogP -0.26 TPSA 94.1	✓ Ro5	✓ Clean	`COCCOCCOCCOCCOCCOCCOCCOCCO`
ZINC34317654	1.000	472.6 Da LogP -0.23 TPSA 112.5	1 viol.	✓ Clean	`COCCOCCOCCOCCOCCOCCOCCOCCOCCOCCO`
ZINC44076059	1.000	428.5 Da LogP -0.24 TPSA 103.3	✓ Ro5	✓ Clean	`COCCOCCOCCOCCOCCOCCOCCOCCOCCO`
ZINC5210101	1.000	252.3 Da LogP -0.31 TPSA 66.4	✓ Ro5	✓ Clean	`COCCOCCOCCOCCOCCO`
ZINC5997860	1.000	296.4 Da LogP -0.29 TPSA 75.6	✓ Ro5	✓ Clean	`COCCOCCOCCOCCOCCOCCO`
ZINC901977	1.000	241.2 Da LogP -0.73 TPSA 127.1	✓ Ro5	Alert	`O=C(N[C@@H](CO)C(=O)O)c1cccc(O)c1O`
ZINC14696227	0.788	225.2 Da LogP -0.43 TPSA 106.9	✓ Ro5	✓ Clean	`O=C(N[C@H](CO)C(=O)O)c1ccccc1O`
ZINC313581	0.769	276.4 Da LogP 2.12 TPSA 59.1	✓ Ro5	✓ Clean	`CCc1ccc(S(=O)(=O)NCc2ccccn2)cc1`
ZINC233866	0.763	263.3 Da LogP 1.14 TPSA 85.1	✓ Ro5	✓ Clean	`Nc1ccc(S(=O)(=O)NCc2ccccn2)cc1`
ZINC29395	0.750	248.3 Da LogP 1.56 TPSA 59.1	✓ Ro5	✓ Clean	`O=S(=O)(NCc1ccccn1)c1ccccc1`
ZINC6699097	0.732	290.4 Da LogP 2.51 TPSA 59.1	✓ Ro5	✓ Clean	`CCCc1ccc(S(=O)(=O)NCc2ccccn2)cc1`
ZINC575419714	0.727	312.4 Da LogP 0.42 TPSA 66.4	✓ Ro5	✓ Clean	`COCCOCCOCCSCCOCCOCCO`
ZINC1158311	0.718	374.2 Da LogP 2.16 TPSA 59.1	✓ Ro5	✓ Clean	`O=S(=O)(NCc1ccccn1)c1ccc(I)cc1`
ZINC145313	0.718	262.3 Da LogP 1.87 TPSA 59.1	✓ Ro5	✓ Clean	`Cc1ccc(S(=O)(=O)NCc2ccccn2)cc1`
ZINC288606	0.718	327.2 Da LogP 2.32 TPSA 59.1	✓ Ro5	✓ Clean	`O=S(=O)(NCc1ccccn1)c1ccc(Br)cc1`
ZINC37689	0.718	266.3 Da LogP 1.70 TPSA 59.1	✓ Ro5	✓ Clean	`O=S(=O)(NCc1ccccn1)c1ccc(F)cc1`
ZINC577388	0.718	282.8 Da LogP 2.21 TPSA 59.1	✓ Ro5	✓ Clean	`O=S(=O)(NCc1ccccn1)c1ccc(Cl)cc1`
ZINC35466170	0.707	255.2 Da LogP -0.64 TPSA 116.1	✓ Ro5	Alert	`COC(=O)[C@@H](CO)NC(=O)c1cccc(O)c1O`
ZINC35466172	0.707	255.2 Da LogP -0.64 TPSA 116.1	✓ Ro5	Alert	`COC(=O)[C@H](CO)NC(=O)c1cccc(O)c1O`
ZINC115163232	0.700	222.3 Da LogP 0.07 TPSA 57.2	✓ Ro5	✓ Clean	`COCCOCCOCCOCCCO`
ZINC258837490	0.700	354.4 Da LogP 0.11 TPSA 84.8	✓ Ro5	✓ Clean	`COCCOCCOCCOCCOCCOCCOCCCO`
ZINC6091714	0.698	369.4 Da LogP -1.11 TPSA 182.2	1 viol.	Alert	`NCCCC[C@@H](NC(=O)c1cccc(O)c1O)C(=O)N[C@@H](CO)…`
ZINC9379229	0.690	291.3 Da LogP 0.66 TPSA 102.2	✓ Ro5	✓ Clean	`NC(=O)c1ccc(S(=O)(=O)NCc2ccccn2)cc1`
ZINC199515761	0.689	446.4 Da LogP 0.18 TPSA 202.7	1 viol.	Alert	`C=C(NC(=O)c1cccc(O)c1O)C(=O)OC[C@H](NC(=O)c1ccc…`
ZINC12501520	0.688	458.5 Da LogP -0.88 TPSA 123.5	1 viol.	✓ Clean	`OCCOCCOCCOCCOCCOCCOCCOCCOCCOCCO`
ZINC1692489	0.688	222.3 Da LogP 0.33 TPSA 46.2	✓ Ro5	✓ Clean	`COCCOCCOCCOCCOC`
ZINC3874716	0.688	414.5 Da LogP -0.90 TPSA 114.3	✓ Ro5	✓ Clean	`OCCOCCOCCOCCOCCOCCOCCOCCOCCO`
ZINC4283769	0.688	238.3 Da LogP -0.96 TPSA 77.4	✓ Ro5	✓ Clean	`OCCOCCOCCOCCOCCO`
ZINC4521548	0.688	282.3 Da LogP -0.95 TPSA 86.6	✓ Ro5	✓ Clean	`OCCOCCOCCOCCOCCOCCO`
ZINC4530388	0.688	266.3 Da LogP 0.35 TPSA 55.4	✓ Ro5	✓ Clean	`COCCOCCOCCOCCOCCOC`
ZINC5178829	0.688	326.4 Da LogP -0.93 TPSA 95.8	✓ Ro5	✓ Clean	`OCCOCCOCCOCCOCCOCCOCCO`
ZINC5178830	0.688	370.4 Da LogP -0.91 TPSA 105.1	✓ Ro5	✓ Clean	`OCCOCCOCCOCCOCCOCCOCCOCCO`
ZINC5701172	0.688	310.4 Da LogP 0.36 TPSA 64.6	✓ Ro5	✓ Clean	`COCCOCCOCCOCCOCCOCCOC`
ZINC5997861	0.688	398.5 Da LogP 0.40 TPSA 83.1	✓ Ro5	✓ Clean	`COCCOCCOCCOCCOCCOCCOCCOCCOC`
ZINC384532	0.683	304.4 Da LogP 2.86 TPSA 59.1	✓ Ro5	✓ Clean	`CC(C)(C)c1ccc(S(=O)(=O)NCc2ccccn2)cc1`
ZINC465808	0.683	338.4 Da LogP 3.54 TPSA 59.1	✓ Ro5	✓ Clean	`Cc1ccc(-c2ccc(S(=O)(=O)NCc3ccccn3)cc2)cc1`
ZINC1079538	0.667	294.4 Da LogP 2.28 TPSA 59.1	✓ Ro5	✓ Clean	`CSc1ccc(S(=O)(=O)NCc2ccccn2)cc1`
ZINC272459	0.667	293.3 Da LogP 1.47 TPSA 102.2	✓ Ro5	✓ Clean	`O=[N+]([O-])c1ccc(S(=O)(=O)NCc2ccccn2)cc1`
ZINC29436	0.667	278.3 Da LogP 1.57 TPSA 68.3	✓ Ro5	✓ Clean	`COc1ccc(S(=O)(=O)NCc2ccccn2)cc1`
ZINC387197	0.667	340.4 Da LogP 3.35 TPSA 68.3	✓ Ro5	✓ Clean	`O=S(=O)(NCc1ccccn1)c1ccc(Oc2ccccc2)cc1`
ZINC5520882	0.667	292.3 Da LogP 1.26 TPSA 96.4	✓ Ro5	✓ Clean	`O=C(O)c1ccc(S(=O)(=O)NCc2ccccn2)cc1`
ZINC575432150	0.667	344.4 Da LogP -0.89 TPSA 100.5	✓ Ro5	✓ Clean	`COCCOCCOCCS(=O)(=O)CCOCCOCCO`
ZINC7059593	0.667	273.3 Da LogP 1.43 TPSA 82.8	✓ Ro5	✓ Clean	`N#Cc1ccc(S(=O)(=O)NCc2ccccn2)cc1`
ZINC7059614	0.667	316.3 Da LogP 2.58 TPSA 59.1	✓ Ro5	✓ Clean	`O=S(=O)(NCc1ccccn1)c1ccc(C(F)(F)F)cc1`
ZINC937452	0.667	358.9 Da LogP 3.88 TPSA 59.1	✓ Ro5	✓ Clean	`O=S(=O)(NCc1ccccn1)c1ccc(-c2ccc(Cl)cc2)cc1`
ZINC1857524240	0.652	207.3 Da LogP -0.75 TPSA 60.0	✓ Ro5	✓ Clean	`COCCNCCOCCOCCO`
ZINC13947769	0.651	304.4 Da LogP 3.07 TPSA 59.1	✓ Ro5	✓ Clean	`CC[C@@H](C)c1ccc(S(=O)(=O)NCc2ccccn2)cc1`

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.