Protein profile

KP13_04541

Glutathione-binding protein gsiB

Genome: KpKP13

Gene: AHE44416.1 gsiB Structure source: AlphaFold + ColabFold UniProt A0A0H3GTC0

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Amino acids 540

Annotations 5

Features 20

PDB binders 17

Druggability 0.998

Overview

Basic information about this protein and its source genome.

Accession: KP13_04541
Assembly: Klebsiella pneumoniae subsp. pneumoniae Kp13, complete sequence
Gene: AHE44416.1 gsiB
Status: annotated
Amino acids: 540
Structure source: AlphaFold + ColabFold

GO:0043190 A complex for the transport of metabolites into and out of the cell, typically comprised of four domains; two membrane-associated domains and two ATP-binding domains at the intracellular face of the membrane, that form a central pore through the plasma membrane. Each of the four core domains may be encoded as a separate polypeptide or the domains can be fused in any one of a number of ways into multidomain polypeptides. In Bacteria and Archaebacteria, ABC transporters also include substrate binding proteins to bind substrate external to the cytoplasm and deliver it to the transporter. GO:0055085 The process in which a solute is transported across a lipid bilayer, from one side of a membrane to the other. 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:1904680 Enables the transfer of a peptide from one side of a membrane to the other. GO:0015833 The directed movement of peptides, compounds of two or more amino acids where the alpha carboxyl group of one is bound to the alpha amino group of another, 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): N
DEG identity (%): 0.0
Localization: Periplasmic
ColabFold pLDDT: 94.62

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 0.998

Structure A0A0H3GTC0

Pocket Pocket 1

P2Rank 0.702

Structure A0A0H3GTC0

Pocket Pocket 1

ColabFold model

FPocket 0.995 · Pocket 1

P2Rank 0.647 · Pocket 1

Core conservation Conserved core gene

Roary core

CoreCruncher core

Gut microbiome 30 / 4744 genomes with a hit

Normalized 0.006

Sequence

Primary amino-acid sequence viewer.

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

5 GO

Gene Ontology (GO)

GO:0043190 A complex for the transport of metabolites into and out of the cell, typically comprised of four domains; two membrane-associated domains and two ATP-binding domains at the intracellular face of the membrane, that form a central pore through the plasma membrane. Each of the four core domains may be encoded as a separate polypeptide or the domains can be fused in any one of a number of ways into multidomain polypeptides. In Bacteria and Archaebacteria, ABC transporters also include substrate binding proteins to bind substrate external to the cytoplasm and deliver it to the transporter.
GO:0055085 The process in which a solute is transported across a lipid bilayer, from one side of a membrane to the other.
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:1904680 Enables the transfer of a peptide from one side of a membrane to the other.
GO:0015833 The directed movement of peptides, compounds of two or more amino acids where the alpha carboxyl group of one is bound to the alpha amino group of another, 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.

20 records

Show feature table

Start	End	DB	Term	Name
285	507	Gene3D	G3DSA:3.10.105.10	-
18	284	Gene3D	G3DSA:3.40.190.10	-
1	23	SignalP_GRAM_NEGATIVE	SignalP-noTM	SignalP-noTM
24	540	Phobius	NON_CYTOPLASMIC_DOMAIN	Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
32	538	NCBIfam	TIGR04028	TIGR04028 family ABC transporter substrate-binding protein
32	538	InterPro	IPR023920	ABC transporter, substrate-binding protein, KPN01854
9	537	PANTHER	PTHR30290	PERIPLASMIC BINDING COMPONENT OF ABC TRANSPORTER
9	537	InterPro	IPR039424	Solute-binding protein family 5
1	23	Phobius	SIGNAL_PEPTIDE	Signal peptide region
5	539	PIRSF	PIRSF002741	MppA
5	539	InterPro	IPR030678	Peptide/nickel binding protein, MppA-type
1	23	SignalP_GRAM_POSITIVE	SignalP-TM	SignalP-TM
1	6	Phobius	SIGNAL_PEPTIDE_N_REGION	N-terminal region of a signal peptide.
74	443	Pfam	PF00496	Bacterial extracellular solute-binding proteins, family 5 Middle
74	443	InterPro	IPR000914	Solute-binding protein family 5 domain
27	538	SUPERFAMILY	SSF53850	Periplasmic binding protein-like II
7	24	TMHMM	TMhelix	Region of a membrane-bound protein predicted to be embedded in the membrane.
7	18	Phobius	SIGNAL_PEPTIDE_H_REGION	Hydrophobic region of a signal peptide.
30	522	CDD	cd08492	PBP2_NikA_DppA_OppA_like_15
19	23	Phobius	SIGNAL_PEPTIDE_C_REGION	C-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_A0A0H3GTC0	AlphaFold	—	—	full sequence	—	Viewing
ColabFold KP13_04541	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				0.998

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	10.33	0.555
2	6.82	0.349
3	1.72	0.03

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				0.995
2				0.635

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	10.11	0.544
2	5.84	0.285
3	1.54	0.023

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.

67 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
6RP	5L8D	P33590	192.2 Da LogP 0.21 TPSA 72.9	✓ Ro5	✓ Clean	`c1cnn(c1)C(C(=O)O)n2cccn2`
8UX	5YH8	Q2FVE7	328.3 Da LogP -1.10 TPSA 164.6	1 viol.	✓ Clean	`C[C@@H](C(=O)O)N[C@@H](CCN[C@H](Cc1c[nH]cn1)C(=…`
9YH	5ON0	P33590	448.5 Da LogP 2.60 TPSA 110.5	✓ Ro5	Alert	`COc1cccc(c1O)CN(CCN(Cc2ccccc2SC)CC(=O)O)CC(=O)O`
9YK	5ON1	P33590	434.5 Da LogP 2.29 TPSA 121.5	✓ Ro5	Alert	`CSc1ccccc1CN(CCN(Cc2cccc(c2O)O)CC(=O)O)CC(=O)O`
BHN	3MVZ	P33590	388.4 Da LogP 1.57 TPSA 121.5	✓ Ro5	Alert	`c1ccc(c(c1)C[N@@](CC[N@](Cc2ccccc2O)CC(=O)O)CC(…`
BHR	3MW0	P33590	404.4 Da LogP 1.28 TPSA 141.8	✓ Ro5	Alert	`c1ccc(c(c1)C[N@@](CC[N@](Cc2cccc(c2O)O)CC(=O)O)…`
BHZ	3MVW	P33590	372.4 Da LogP 1.87 TPSA 101.3	✓ Ro5	Alert	`c1ccc(cc1)C[N@@](CC[N@](Cc2ccccc2O)CC(=O)O)CC(=…`
CMO	5L8D	P33590	28.0 Da LogP -0.04 TPSA 19.9	✓ Ro5	✓ Clean	`[C-]#[O+]`
DTD	3MW0	P33590	152.2 Da LogP 0.10 TPSA 40.5	✓ Ro5	✓ Clean	`C1[C@@H]([C@H](CSS1)O)O`
DTT	1ZLQ	P33590	154.3 Da LogP -0.43 TPSA 40.5	✓ Ro5	✓ Clean	`C([C@@H]([C@H](CS)O)O)S`
DTU	3MVX	P33590	154.3 Da LogP -0.43 TPSA 40.5	✓ Ro5	✓ Clean	`C([C@H]([C@H](CS)O)O)S`
DTV	3MVX	P33590	154.3 Da LogP -0.43 TPSA 40.5	✓ Ro5	✓ Clean	`C([C@H]([C@@H](CS)O)O)S`
EDT	1ZLQ	P33590	292.2 Da LogP -2.07 TPSA 155.7	✓ Ro5	✓ Clean	`C(CN(CC(=O)O)CC(=O)O)N(CC(=O)O)CC(=O)O`
GDS	3M8U	B8F653	612.6 Da LogP -3.88 TPSA 317.6	3 viol.	✓ Clean	`C(CC(=O)N[C@@H](CSSC[C@@H](C(=O)NCC(=O)O)NC(=O)…`
HCT	3DP8	P33590	190.2 Da LogP 0.03 TPSA 111.9	✓ Ro5	✓ Clean	`C(CC(=O)O)[C@H](CC(=O)O)C(=O)O`
MLI	3M8U	B8F653	102.0 Da LogP -3.12 TPSA 80.3	✓ Ro5	✓ Clean	`C(C(=O)[O-])C(=O)[O-]`
PER	3MVZ	P33590	32.0 Da LogP -2.38 TPSA 46.1	✓ Ro5	✓ Clean	`[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
ZINC19364242	1.000	292.2 Da LogP -2.07 TPSA 155.7	✓ Ro5	✓ Clean	`O=C(O)CN(CCN(CC(=O)O)CC(=O)O)CC(=O)O`
ZINC19419017	0.933	393.3 Da LogP -2.68 TPSA 196.2	✓ Ro5	✓ Clean	`O=C(O)CN(CCN(CC(=O)O)CC(=O)O)CCN(CC(=O)O)CC(=O)O`
ZINC22593216	0.933	494.5 Da LogP -3.30 TPSA 236.8	1 viol.	✓ Clean	`O=C(O)CN(CCN(CCN(CC(=O)O)CC(=O)O)CC(=O)O)CCN(CC…`
ZINC4556980	0.825	321.4 Da LogP -1.77 TPSA 158.8	✓ Ro5	✓ Clean	`CSC[C@H](NC(=O)CC[C@@H](N)C(=O)O)C(=O)NCC(=O)O`
ZINC13522300	0.767	349.4 Da LogP -1.86 TPSA 175.9	✓ Ro5	✓ Clean	`CC(=O)SC[C@H](NC(=O)CC[C@H](N)C(=O)O)C(=O)NCC(=…`
ZINC31350707	0.767	349.4 Da LogP -1.86 TPSA 175.9	✓ Ro5	✓ Clean	`CC(=O)SC[C@@H](NC(=O)CC[C@@H](N)C(=O)O)C(=O)NCC…`
ZINC31350710	0.767	349.4 Da LogP -1.86 TPSA 175.9	✓ Ro5	✓ Clean	`CC(=O)SC[C@H](NC(=O)CC[C@@H](N)C(=O)O)C(=O)NCC(…`
ZINC31350713	0.767	349.4 Da LogP -1.86 TPSA 175.9	✓ Ro5	✓ Clean	`CC(=O)SC[C@@H](NC(=O)CC[C@H](N)C(=O)O)C(=O)NCC(…`
ZINC3872731	0.767	336.3 Da LogP -1.72 TPSA 188.2	✓ Ro5	✓ Clean	`N[C@@H](CCC(=O)N[C@@H](CSN=O)C(=O)NCC(=O)O)C(=O…`
ZINC3872732	0.767	336.3 Da LogP -1.72 TPSA 188.2	✓ Ro5	✓ Clean	`N[C@@H](CCC(=O)N[C@H](CSN=O)C(=O)NCC(=O)O)C(=O)O`
ZINC3872733	0.767	336.3 Da LogP -1.72 TPSA 188.2	✓ Ro5	✓ Clean	`N[C@H](CCC(=O)N[C@@H](CSN=O)C(=O)NCC(=O)O)C(=O)O`
ZINC3872734	0.767	336.3 Da LogP -1.72 TPSA 188.2	✓ Ro5	✓ Clean	`N[C@H](CCC(=O)N[C@H](CSN=O)C(=O)NCC(=O)O)C(=O)O`
ZINC4544082	0.767	335.4 Da LogP -1.38 TPSA 158.8	✓ Ro5	✓ Clean	`CCSC[C@H](NC(=O)CC[C@H](N)C(=O)O)C(=O)NCC(=O)O`
ZINC4544083	0.767	335.4 Da LogP -1.38 TPSA 158.8	✓ Ro5	✓ Clean	`CCSC[C@@H](NC(=O)CC[C@H](N)C(=O)O)C(=O)NCC(=O)O`
ZINC4544084	0.767	335.4 Da LogP -1.38 TPSA 158.8	✓ Ro5	✓ Clean	`CCSC[C@H](NC(=O)CC[C@@H](N)C(=O)O)C(=O)NCC(=O)O`
ZINC4544085	0.767	335.4 Da LogP -1.38 TPSA 158.8	✓ Ro5	✓ Clean	`CCSC[C@@H](NC(=O)CC[C@@H](N)C(=O)O)C(=O)NCC(=O)O`
ZINC1769289	0.765	306.3 Da LogP -1.68 TPSA 155.7	✓ Ro5	✓ Clean	`O=C(O)CN(CCCN(CC(=O)O)CC(=O)O)CC(=O)O`
ZINC4683946	0.765	320.3 Da LogP -1.29 TPSA 155.7	✓ Ro5	✓ Clean	`O=C(O)CN(CCCCN(CC(=O)O)CC(=O)O)CC(=O)O`
ZINC13451235	0.750	423.4 Da LogP -2.47 TPSA 233.4	1 viol.	✓ Clean	`N[C@@H](CCC(=O)N[C@@H](CS[C@H](CC(=O)O)C(=O)O)C…`
ZINC145953214	0.750	365.4 Da LogP -2.02 TPSA 179.0	1 viol.	✓ Clean	`C[C@H](O)CSC[C@@H](NC(=O)CC[C@@H](N)C(=O)O)C(=O…`
ZINC145953600	0.750	365.4 Da LogP -2.02 TPSA 179.0	1 viol.	✓ Clean	`C[C@H](O)CSC[C@H](NC(=O)CC[C@@H](N)C(=O)O)C(=O)…`
ZINC14966489	0.750	423.4 Da LogP -2.47 TPSA 233.4	1 viol.	✓ Clean	`N[C@H](CCC(=O)N[C@@H](CS[C@@H](CC(=O)O)C(=O)O)C…`
ZINC14966492	0.750	423.4 Da LogP -2.47 TPSA 233.4	1 viol.	✓ Clean	`N[C@H](CCC(=O)N[C@H](CS[C@@H](CC(=O)O)C(=O)O)C(…`
ZINC1690029	0.750	204.2 Da LogP 0.42 TPSA 111.9	✓ Ro5	✓ Clean	`O=C(O)CCC(CCC(=O)O)C(=O)O`
ZINC201224060	0.750	365.4 Da LogP -2.02 TPSA 179.0	1 viol.	✓ Clean	`C[C@H](O)CSC[C@@H](NC(=O)CC[C@H](N)C(=O)O)C(=O)…`
ZINC253638410	0.750	423.4 Da LogP -2.47 TPSA 233.4	1 viol.	✓ Clean	`N[C@H](CCC(=O)N[C@H](CS[C@H](CC(=O)O)C(=O)O)C(=…`
ZINC253638411	0.750	423.4 Da LogP -2.47 TPSA 233.4	1 viol.	✓ Clean	`N[C@H](CCC(=O)N[C@@H](CS[C@H](CC(=O)O)C(=O)O)C(…`
ZINC3920510	0.750	423.4 Da LogP -2.47 TPSA 233.4	1 viol.	✓ Clean	`N[C@@H](CCC(=O)N[C@@H](CS[C@@H](CC(=O)O)C(=O)O)…`
ZINC77300920	0.750	365.4 Da LogP -2.02 TPSA 179.0	1 viol.	✓ Clean	`C[C@H](O)CSC[C@H](NC(=O)CC[C@H](N)C(=O)O)C(=O)N…`
ZINC19364891	0.737	204.2 Da LogP -0.98 TPSA 81.1	✓ Ro5	✓ Clean	`CN(C)CCN(CC(=O)O)CC(=O)O`
ZINC19364892	0.737	232.3 Da LogP -0.20 TPSA 81.1	✓ Ro5	✓ Clean	`CCN(CC)CCN(CC(=O)O)CC(=O)O`
ZINC19366122	0.737	278.3 Da LogP -2.16 TPSA 138.6	✓ Ro5	✓ Clean	`O=C(O)CN(CCO)CCN(CC(=O)O)CC(=O)O`
ZINC33806192	0.737	320.3 Da LogP -1.29 TPSA 155.7	✓ Ro5	✓ Clean	`O=C(O)CCN(CCC(=O)O)CCN(CC(=O)O)CC(=O)O`
ZINC5908834	0.737	379.3 Da LogP -2.09 TPSA 196.2	✓ Ro5	✓ Clean	`O=C(O)CN(CCN(CCN(CC(=O)O)CC(=O)O)C(=O)O)CC(=O)O`
ZINC3870222	0.733	379.4 Da LogP -2.50 TPSA 196.1	1 viol.	✓ Clean	`C[C@H](O)C(=O)SC[C@H](NC(=O)CC[C@H](N)C(=O)O)C(…`
ZINC4556756	0.733	377.4 Da LogP -2.29 TPSA 193.0	✓ Ro5	✓ Clean	`CC(=O)C(=O)SC[C@H](NC(=O)CC[C@H](N)C(=O)O)C(=O)…`
ZINC4556757	0.733	377.4 Da LogP -2.29 TPSA 193.0	✓ Ro5	✓ Clean	`CC(=O)C(=O)SC[C@@H](NC(=O)CC[C@H](N)C(=O)O)C(=O…`
ZINC4556758	0.733	377.4 Da LogP -2.29 TPSA 193.0	✓ Ro5	✓ Clean	`CC(=O)C(=O)SC[C@H](NC(=O)CC[C@@H](N)C(=O)O)C(=O…`
ZINC4556759	0.733	377.4 Da LogP -2.29 TPSA 193.0	✓ Ro5	✓ Clean	`CC(=O)C(=O)SC[C@@H](NC(=O)CC[C@@H](N)C(=O)O)C(=…`
ZINC4962281	0.733	349.4 Da LogP -0.99 TPSA 158.8	✓ Ro5	✓ Clean	`CCCSC[C@H](NC(=O)CC[C@H](N)C(=O)O)C(=O)NCC(=O)O`
ZINC504173140	0.733	365.4 Da LogP -2.02 TPSA 179.0	1 viol.	✓ Clean	`C[C@H](CO)SC[C@H](NC(=O)CC[C@@H](N)C(=O)O)C(=O)…`
ZINC504173141	0.733	365.4 Da LogP -2.02 TPSA 179.0	1 viol.	✓ Clean	`C[C@H](CO)SC[C@@H](NC(=O)CC[C@H](N)C(=O)O)C(=O)…`
ZINC504173142	0.733	365.4 Da LogP -2.02 TPSA 179.0	1 viol.	✓ Clean	`C[C@H](CO)SC[C@@H](NC(=O)CC[C@@H](N)C(=O)O)C(=O…`
ZINC5883749	0.733	364.4 Da LogP -2.06 TPSA 187.9	1 viol.	✓ Clean	`CNC(=O)SC[C@H](NC(=O)CC[C@H](N)C(=O)O)C(=O)NCC(…`
ZINC5883751	0.733	364.4 Da LogP -2.06 TPSA 187.9	1 viol.	✓ Clean	`CNC(=O)SC[C@@H](NC(=O)CC[C@H](N)C(=O)O)C(=O)NCC…`
ZINC5883754	0.733	364.4 Da LogP -2.06 TPSA 187.9	1 viol.	✓ Clean	`CNC(=O)SC[C@H](NC(=O)CC[C@@H](N)C(=O)O)C(=O)NCC…`
ZINC5883758	0.733	364.4 Da LogP -2.06 TPSA 187.9	1 viol.	✓ Clean	`CNC(=O)SC[C@@H](NC(=O)CC[C@@H](N)C(=O)O)C(=O)NC…`
ZINC77300937	0.733	365.4 Da LogP -2.02 TPSA 179.0	1 viol.	✓ Clean	`C[C@H](CO)SC[C@H](NC(=O)CC[C@H](N)C(=O)O)C(=O)N…`
ZINC3830891	0.732	307.3 Da LogP -2.21 TPSA 158.8	1 viol.	✓ Clean	`N[C@@H](CCC(=O)N[C@@H](CS)C(=O)NCC(=O)O)C(=O)O`
ZINC3830894	0.732	307.3 Da LogP -2.21 TPSA 158.8	1 viol.	✓ Clean	`N[C@H](CCC(=O)N[C@H](CS)C(=O)NCC(=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.