Protein profile

KP13_01170

Spermidine export protein mdtI

Genome: KpKP13

Gene: AHE44753.1 mdtI Structure source: AlphaFold + ColabFold UniProt A0A0H3GPF5

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Amino acids 109

Annotations 5

Features 22

PDB binders 0

Druggability 0.881

Overview

Basic information about this protein and its source genome.

Accession: KP13_01170
Assembly: Klebsiella pneumoniae subsp. pneumoniae Kp13, complete sequence
Gene: AHE44753.1 mdtI
Status: annotated
Amino acids: 109
Structure source: AlphaFold + ColabFold

GO:0005886 The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins. GO:0015848 The directed movement of spermidine, N-(3-aminopropyl)-1,4-diaminobutane, a polyamine formed by the transfer of a propylamine group from decarboxylated S-adenosylmethionine to putrescine, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. GO:0022857 Enables the transfer of a substance, usually a specific substance or a group of related substances, from one side of a membrane to the other. GO:0016020 A lipid bilayer along with all the proteins and protein complexes embedded in it and attached to it. GO:0015606 Enables the transfer of spermidine, N-(3-aminopropyl)-1,4-diaminobutane, 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): Y
DEG identity (%): 84.404
DEG E-value: 8.14e-57
Localization: CytoplasmicMembrane
ColabFold pLDDT: 90.98

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 0.881

Structure A0A0H3GPF5

Pocket Pocket 3

P2Rank

Structure A0A0H3GPF5

Pocket No pockets

ColabFold model

FPocket 0.583 · Pocket 3

P2Rank 0.005 · Pocket 1

Core conservation Accessory gene

Roary accessory

CoreCruncher accessory

Gut microbiome 122 / 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.

5 GO

Gene Ontology (GO)

GO:0005886 The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.
GO:0015848 The directed movement of spermidine, N-(3-aminopropyl)-1,4-diaminobutane, a polyamine formed by the transfer of a propylamine group from decarboxylated S-adenosylmethionine to putrescine, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
GO:0022857 Enables the transfer of a substance, usually a specific substance or a group of related substances, from one side of a membrane to the other.
GO:0016020 A lipid bilayer along with all the proteins and protein complexes embedded in it and attached to it.
GO:0015606 Enables the transfer of spermidine, N-(3-aminopropyl)-1,4-diaminobutane, from one side of a membrane to the other.

Sequence Features

Domain/signature hits from InterPro and related databases.

22 records

Show feature table

Start	End	DB	Term	Name
85	90	Phobius	CYTOPLASMIC_DOMAIN	Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
109	109	Phobius	NON_CYTOPLASMIC_DOMAIN	Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
5	109	FunFam	G3DSA:1.10.3730.20:FF:000001	Quaternary ammonium compound resistance transporter SugE
92	106	TMHMM	TMhelix	Region of a membrane-bound protein predicted to be embedded in the membrane.
6	25	Phobius	TRANSMEMBRANE	Region of a membrane-bound protein predicted to be embedded in the membrane.
10	29	TMHMM	TMhelix	Region of a membrane-bound protein predicted to be embedded in the membrane.
57	61	Phobius	NON_CYTOPLASMIC_DOMAIN	Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
91	108	Phobius	TRANSMEMBRANE	Region of a membrane-bound protein predicted to be embedded in the membrane.
37	56	Phobius	TRANSMEMBRANE	Region of a membrane-bound protein predicted to be embedded in the membrane.
62	84	Phobius	TRANSMEMBRANE	Region of a membrane-bound protein predicted to be embedded in the membrane.
5	99	Pfam	PF00893	Small Multidrug Resistance protein
5	99	InterPro	IPR045324	Small multidrug resistance protein
1	109	Hamap	MF_01597	Spermidine export protein MdtI [mdtI].
1	109	InterPro	IPR023737	Spermidine export protein MdtI
1	5	Phobius	NON_CYTOPLASMIC_DOMAIN	Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
12	108	SUPERFAMILY	SSF103481	Multidrug resistance efflux transporter EmrE
26	36	Phobius	CYTOPLASMIC_DOMAIN	Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
63	85	TMHMM	TMhelix	Region of a membrane-bound protein predicted to be embedded in the membrane.
10	108	PANTHER	PTHR30561	SMR FAMILY PROTON-DEPENDENT DRUG EFFLUX TRANSPORTER SUGE
10	108	InterPro	IPR000390	Small drug/metabolite transporter protein family
36	53	TMHMM	TMhelix	Region of a membrane-bound protein predicted to be embedded in the membrane.
7	109	Gene3D	G3DSA:1.10.3730.20	-

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_A0A0H3GPF5	AlphaFold	—	—	full sequence	—	Viewing
ColabFold KP13_01170	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
3				0.881
4				0.364
1				0.343

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				0.583
1				0.288

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.

54 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.

No PDB ligands found through similar proteins.

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).

Ligand	UniProt (homolog)	pchembl	MW · LogP · TPSA	Lipinski	PAINS	SMILES
CHEMBL891	Q3S5C3	8.40	435.9 Da LogP 2.55 TPSA 112.7	✓ Ro5	✓ Clean	`Cc1onc(-c2ccccc2Cl)c1C(=O)N[C@@H]1C(=O)N2[C@@H]…`
CHEMBL158	Q3S5C3	8.22	435.4 Da LogP -1.17 TPSA 201.6	✓ Ro5	✓ Clean	`C[C@H]1[C@H](NC(=O)/C(=N\OC(C)(C)C(=O)O)c2csc(N…`
CHEMBL333078	Q3S5C3	6.52	270.3 Da LogP -0.74 TPSA 115.5	✓ Ro5	✓ Clean	`C[C@]1(/C=C\C#N)[C@H](C(=O)O)N2C(=O)C[C@H]2S1(=…`
CHEMBL224214	Q2FD83	—	204.6 Da LogP 2.16 TPSA 72.0	✓ Ro5	Alert	`N#CC(C#N)=NNc1cccc(Cl)c1`

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
ZINC15848211	1.000	435.4 Da LogP -1.17 TPSA 201.6	✓ Ro5	✓ Clean	`C[C@@H]1[C@H](NC(=O)/C(=N\OC(C)(C)C(=O)O)c2csc(…`
ZINC161387	1.000	204.6 Da LogP 2.16 TPSA 72.0	✓ Ro5	Alert	`N#CC(C#N)=NNc1cccc(Cl)c1`
ZINC16958002	1.000	435.4 Da LogP -1.17 TPSA 201.6	✓ Ro5	✓ Clean	`C[C@H]1[C@@H](NC(=O)/C(=N/OC(C)(C)C(=O)O)c2csc(…`
ZINC17214369	1.000	435.4 Da LogP -1.17 TPSA 201.6	✓ Ro5	✓ Clean	`C[C@@H]1[C@@H](NC(=O)/C(=N/OC(C)(C)C(=O)O)c2csc…`
ZINC21986197	1.000	435.9 Da LogP 2.55 TPSA 112.7	✓ Ro5	✓ Clean	`Cc1onc(-c2ccccc2Cl)c1C(=O)N[C@@H]1C(=O)N2[C@H]1…`
ZINC252430978	1.000	435.4 Da LogP -1.17 TPSA 201.6	✓ Ro5	✓ Clean	`C[C@H]1[C@H](NC(=O)C(=NOC(C)(C)C(=O)O)c2csc(N)n…`
ZINC256010240	1.000	435.4 Da LogP -1.17 TPSA 201.6	✓ Ro5	✓ Clean	`C[C@H]1[C@@H](NC(=O)C(=NOC(C)(C)C(=O)O)c2csc(N)…`
ZINC256010241	1.000	435.4 Da LogP -1.17 TPSA 201.6	✓ Ro5	✓ Clean	`C[C@@H]1[C@@H](NC(=O)C(=NOC(C)(C)C(=O)O)c2csc(N…`
ZINC256010242	1.000	435.4 Da LogP -1.17 TPSA 201.6	✓ Ro5	✓ Clean	`C[C@@H]1[C@H](NC(=O)C(=NOC(C)(C)C(=O)O)c2csc(N)…`
ZINC3830263	1.000	435.4 Da LogP -1.17 TPSA 201.6	✓ Ro5	✓ Clean	`C[C@@H]1[C@H](NC(=O)/C(=N/OC(C)(C)C(=O)O)c2csc(…`
ZINC3830264	1.000	435.4 Da LogP -1.17 TPSA 201.6	✓ Ro5	✓ Clean	`C[C@H]1[C@H](NC(=O)/C(=N\OC(C)(C)C(=O)O)c2csc(N…`
ZINC3830266	1.000	435.4 Da LogP -1.17 TPSA 201.6	✓ Ro5	✓ Clean	`C[C@H]1[C@@H](NC(=O)/C(=N\OC(C)(C)C(=O)O)c2csc(…`
ZINC3830593	1.000	435.9 Da LogP 2.55 TPSA 112.7	✓ Ro5	✓ Clean	`Cc1onc(-c2ccccc2Cl)c1C(=O)N[C@@H]1C(=O)N2[C@@H]…`
ZINC3830594	1.000	435.9 Da LogP 2.55 TPSA 112.7	✓ Ro5	✓ Clean	`Cc1onc(-c2ccccc2Cl)c1C(=O)N[C@H]1C(=O)N2[C@H]1S…`
ZINC3830595	1.000	435.9 Da LogP 2.55 TPSA 112.7	✓ Ro5	✓ Clean	`Cc1onc(-c2ccccc2Cl)c1C(=O)N[C@@H]1C(=O)N2[C@H]1…`
ZINC3875417	1.000	435.9 Da LogP 2.55 TPSA 112.7	✓ Ro5	✓ Clean	`Cc1onc(-c2ccccc2Cl)c1C(=O)N[C@@H]1C(=O)N2[C@@H]…`
ZINC4676362	1.000	435.4 Da LogP -1.17 TPSA 201.6	✓ Ro5	✓ Clean	`C[C@@H]1[C@@H](NC(=O)/C(=N\OC(C)(C)C(=O)O)c2csc…`
ZINC1530612	0.839	470.3 Da LogP 3.20 TPSA 112.7	✓ Ro5	✓ Clean	`Cc1onc(-c2c(Cl)cccc2Cl)c1C(=O)N[C@H]1C(=O)N2[C@…`
ZINC2015281	0.839	470.3 Da LogP 3.20 TPSA 112.7	✓ Ro5	✓ Clean	`Cc1onc(-c2c(Cl)cccc2Cl)c1C(=O)N[C@@H]1C(=O)N2[C…`
ZINC3830690	0.839	470.3 Da LogP 3.20 TPSA 112.7	✓ Ro5	✓ Clean	`Cc1onc(-c2c(Cl)cccc2Cl)c1C(=O)N[C@@H]1C(=O)N2[C…`
ZINC3830691	0.839	470.3 Da LogP 3.20 TPSA 112.7	✓ Ro5	✓ Clean	`Cc1onc(-c2c(Cl)cccc2Cl)c1C(=O)N[C@H]1C(=O)N2[C@…`
ZINC3830692	0.839	470.3 Da LogP 3.20 TPSA 112.7	✓ Ro5	✓ Clean	`Cc1onc(-c2c(Cl)cccc2Cl)c1C(=O)N[C@@H]1C(=O)N2[C…`
ZINC3978006	0.839	470.3 Da LogP 3.20 TPSA 112.7	✓ Ro5	✓ Clean	`Cc1onc(-c2c(Cl)cccc2Cl)c1C(=O)N[C@@H]1C(=O)N2[C…`
ZINC1532344	0.800	453.9 Da LogP 2.69 TPSA 112.7	✓ Ro5	✓ Clean	`Cc1onc(-c2c(F)cccc2Cl)c1C(=O)N[C@H]1C(=O)N2[C@@…`
ZINC3830843	0.800	453.9 Da LogP 2.69 TPSA 112.7	✓ Ro5	✓ Clean	`Cc1onc(-c2c(F)cccc2Cl)c1C(=O)N[C@@H]1C(=O)N2[C@…`
ZINC3830844	0.800	453.9 Da LogP 2.69 TPSA 112.7	✓ Ro5	✓ Clean	`Cc1onc(-c2c(F)cccc2Cl)c1C(=O)N[C@H]1C(=O)N2[C@H…`
ZINC3830845	0.800	453.9 Da LogP 2.69 TPSA 112.7	✓ Ro5	✓ Clean	`Cc1onc(-c2c(F)cccc2Cl)c1C(=O)N[C@@H]1C(=O)N2[C@…`
ZINC4102187	0.800	453.9 Da LogP 2.69 TPSA 112.7	✓ Ro5	✓ Clean	`Cc1onc(-c2c(F)cccc2Cl)c1C(=O)N[C@@H]1C(=O)N2[C@…`
ZINC9230633	0.800	453.9 Da LogP 2.69 TPSA 112.7	✓ Ro5	✓ Clean	`Cc1onc(-c2c(F)cccc2Cl)c1C(=O)N[C@@H]1C(=O)N2[C@…`
ZINC3831241	0.790	401.4 Da LogP 1.90 TPSA 112.7	✓ Ro5	✓ Clean	`Cc1onc(-c2ccccc2)c1C(=O)N[C@@H]1C(=O)N2[C@@H]1S…`
ZINC3831242	0.790	401.4 Da LogP 1.90 TPSA 112.7	✓ Ro5	✓ Clean	`Cc1onc(-c2ccccc2)c1C(=O)N[C@H]1C(=O)N2[C@H]1SC(…`
ZINC3831243	0.790	401.4 Da LogP 1.90 TPSA 112.7	✓ Ro5	✓ Clean	`Cc1onc(-c2ccccc2)c1C(=O)N[C@@H]1C(=O)N2[C@H]1SC…`
ZINC3875439	0.790	401.4 Da LogP 1.90 TPSA 112.7	✓ Ro5	✓ Clean	`Cc1onc(-c2ccccc2)c1C(=O)N[C@@H]1C(=O)N2[C@@H](C…`
ZINC9212279	0.790	401.4 Da LogP 1.90 TPSA 112.7	✓ Ro5	✓ Clean	`Cc1onc(-c2ccccc2)c1C(=O)N[C@@H]1C(=O)N2[C@H]1SC…`
ZINC148820510	0.781	453.4 Da LogP -1.22 TPSA 201.6	✓ Ro5	✓ Clean	`CC(C)(O/N=C(/C(=O)N[C@@H]1C(=O)N(S(=O)(=O)O)[C@…`
ZINC12503091	0.703	435.4 Da LogP -0.33 TPSA 205.1	✓ Ro5	✓ Clean	`C[C@H]1[C@H](/N=C(O)/C(=N/OC(C)(C)C(=O)O)c2csc(…`
ZINC110918	0.688	239.1 Da LogP 2.81 TPSA 72.0	✓ Ro5	Alert	`N#CC(C#N)=NNc1cc(Cl)cc(Cl)c1`
ZINC1554503643	0.676	260.6 Da LogP 1.29 TPSA 106.1	✓ Ro5	Alert	`N#CC(=O)C(=NNc1cccc(Cl)c1)C(=O)C#N`
ZINC4194526	0.657	249.1 Da LogP 2.26 TPSA 72.0	✓ Ro5	Alert	`N#CC(C#N)=NNc1cccc(Br)c1`
ZINC5427363	0.647	239.1 Da LogP 2.81 TPSA 72.0	✓ Ro5	Alert	`N#CC(C#N)=NNc1ccc(Cl)c(Cl)c1`
ZINC1560410105	0.636	433.4 Da LogP -0.70 TPSA 201.6	✓ Ro5	✓ Clean	`CC1=C(NC(=O)C(=NOC(C)(C)C(=O)O)c2csc(N)n2)C(=O)…`
ZINC204907801	0.629	425.5 Da LogP 0.61 TPSA 147.2	✓ Ro5	✓ Clean	`CC1=CN2C(=O)[C@@H](NC(=O)/C(=N/OC(C)(C)C(=O)O)c…`
ZINC613829019	0.629	425.5 Da LogP 0.61 TPSA 147.2	✓ Ro5	✓ Clean	`CC1=CN2C(=O)[C@@H](NC(=O)C(=NOC(C)(C)C(=O)O)c3c…`
ZINC495173	0.605	238.2 Da LogP 2.52 TPSA 72.0	✓ Ro5	Alert	`N#CC(C#N)=NNc1cccc(C(F)(F)F)c1`
ZINC2086	0.605	233.2 Da LogP -0.79 TPSA 91.8	✓ Ro5	✓ Clean	`CC1(C)[C@@H](C(=O)O)N2C(=O)C[C@H]2S1(=O)=O`
ZINC2548423	0.605	233.2 Da LogP -0.79 TPSA 91.8	✓ Ro5	✓ Clean	`CC1(C)[C@H](C(=O)O)N2C(=O)C[C@@H]2S1(=O)=O`
ZINC336994	0.605	233.2 Da LogP -0.79 TPSA 91.8	✓ Ro5	✓ Clean	`CC1(C)[C@@H](C(=O)O)N2C(=O)C[C@@H]2S1(=O)=O`
ZINC897244	0.605	233.2 Da LogP -0.79 TPSA 91.8	✓ Ro5	✓ Clean	`CC1(C)[C@H](C(=O)O)N2C(=O)C[C@H]2S1(=O)=O`
ZINC13111736	0.595	283.7 Da LogP 3.51 TPSA 65.2	✓ Ro5	Alert	`N#C/C(=N\Nc1cccc(Cl)c1)C(=O)c1ccccc1`
ZINC353283	0.595	318.2 Da LogP 4.17 TPSA 65.2	✓ Ro5	Alert	`N#C/C(=N/Nc1cccc(Cl)c1)C(=O)c1ccc(Cl)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.