Protein profile

KP13_00769

Preprotein translocase subunit secY

Genome: KpKP13

Gene: secY AHE42383.1 Structure source: AlphaFold + ColabFold UniProt A0A0H3GZ91

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Amino acids 443

Annotations 6

Features 59

PDB binders 3

Druggability 0.924

Overview

Basic information about this protein and its source genome.

Accession: KP13_00769
Assembly: Klebsiella pneumoniae subsp. pneumoniae Kp13, complete sequence
Gene: secY AHE42383.1
Status: annotated
Amino acids: 443
Structure source: AlphaFold + ColabFold

GO:0015031 The directed movement of proteins into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. GO:0016020 A lipid bilayer along with all the proteins and protein complexes embedded in it and attached to it. 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:0065002 The directed movement of proteins in a cell, from one side of a membrane to another by means of some agent such as a transporter or pore. GO:0006605 The process of targeting specific proteins to particular regions of the cell, typically membrane-bounded subcellular organelles. Usually requires an organelle specific protein sequence motif. GO:0043952 The process in which unfolded proteins are transported across the cytoplasmic membrane in Gram-positive and Gram-negative bacteria by the Sec complex, in a process involving proteolytic cleavage of an N-terminal signal peptide.

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 (%): 98.194
DEG E-value: 0.0
Localization: CytoplasmicMembrane
ColabFold pLDDT: 78.49

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 0.924

Structure A0A0H3GZ91

Pocket Pocket 44

P2Rank 0.884

Structure A0A0H3GZ91

Pocket Pocket 1

ColabFold model

FPocket 0.928 · Pocket 13

P2Rank 0.903 · Pocket 1

Core conservation Conserved core gene

Roary core

CoreCruncher core

Gut microbiome 313 / 4744 genomes with a hit

Normalized 0.066

Sequence

Primary amino-acid sequence viewer.

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

6 GO

Gene Ontology (GO)

GO:0015031 The directed movement of proteins into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
GO:0016020 A lipid bilayer along with all the proteins and protein complexes embedded in it and attached to it.
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:0065002 The directed movement of proteins in a cell, from one side of a membrane to another by means of some agent such as a transporter or pore.
GO:0006605 The process of targeting specific proteins to particular regions of the cell, typically membrane-bounded subcellular organelles. Usually requires an organelle specific protein sequence motif.
GO:0043952 The process in which unfolded proteins are transported across the cytoplasmic membrane in Gram-positive and Gram-negative bacteria by the Sec complex, in a process involving proteolytic cleavage of an N-terminal signal peptide.

Sequence Features

Domain/signature hits from InterPro and related databases.

59 records

Show feature table

Start	End	DB	Term	Name
15	429	Gene3D	G3DSA:1.10.3370.10	SecY subunit domain
15	429	InterPro	IPR023201	SecY domain superfamily
397	418	Phobius	TRANSMEMBRANE	Region of a membrane-bound protein predicted to be embedded in the membrane.
274	296	TMHMM	TMhelix	Region of a membrane-bound protein predicted to be embedded in the membrane.
77	99	TMHMM	TMhelix	Region of a membrane-bound protein predicted to be embedded in the membrane.
45	74	Phobius	NON_CYTOPLASMIC_DOMAIN	Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
316	338	TMHMM	TMhelix	Region of a membrane-bound protein predicted to be embedded in the membrane.
338	372	Phobius	CYTOPLASMIC_DOMAIN	Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
9	429	FunFam	G3DSA:1.10.3370.10:FF:000001	Preprotein translocase subunit SecY
10	433	Hamap	MF_01465	Protein translocase subunit SecY [secY].
10	433	InterPro	IPR026593	Protein translocase subunit SecY
186	203	Phobius	TRANSMEMBRANE	Region of a membrane-bound protein predicted to be embedded in the membrane.
274	296	Phobius	TRANSMEMBRANE	Region of a membrane-bound protein predicted to be embedded in the membrane.
204	214	Phobius	NON_CYTOPLASMIC_DOMAIN	Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
419	443	Phobius	CYTOPLASMIC_DOMAIN	Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
392	396	Phobius	NON_CYTOPLASMIC_DOMAIN	Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
76	95	ProSitePatterns	PS00755	Protein secY signature 1.
76	95	InterPro	IPR030659	SecY conserved site
175	185	Phobius	CYTOPLASMIC_DOMAIN	Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
397	414	TMHMM	TMhelix	Region of a membrane-bound protein predicted to be embedded in the membrane.
20	429	NCBIfam	TIGR00967	preprotein translocase subunit SecY
20	429	InterPro	IPR002208	SecY/SEC61-alpha family
76	417	Pfam	PF00344	SecY
76	417	InterPro	IPR002208	SecY/SEC61-alpha family
215	237	TMHMM	TMhelix	Region of a membrane-bound protein predicted to be embedded in the membrane.
373	391	Phobius	TRANSMEMBRANE	Region of a membrane-bound protein predicted to be embedded in the membrane.
1	22	Phobius	CYTOPLASMIC_DOMAIN	Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
316	337	Phobius	TRANSMEMBRANE	Region of a membrane-bound protein predicted to be embedded in the membrane.
182	204	TMHMM	TMhelix	Region of a membrane-bound protein predicted to be embedded in the membrane.
75	99	Phobius	TRANSMEMBRANE	Region of a membrane-bound protein predicted to be embedded in the membrane.
238	273	Phobius	CYTOPLASMIC_DOMAIN	Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
23	44	Phobius	TRANSMEMBRANE	Region of a membrane-bound protein predicted to be embedded in the membrane.
16	424	SUPERFAMILY	SSF103491	Preprotein translocase SecY subunit
16	424	InterPro	IPR023201	SecY domain superfamily
153	175	TMHMM	TMhelix	Region of a membrane-bound protein predicted to be embedded in the membrane.
140	153	Phobius	NON_CYTOPLASMIC_DOMAIN	Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
22	44	TMHMM	TMhelix	Region of a membrane-bound protein predicted to be embedded in the membrane.
11	441	PIRSF	PIRSF004557	SecY_Sec61alpha
11	441	InterPro	IPR002208	SecY/SEC61-alpha family
100	118	Phobius	CYTOPLASMIC_DOMAIN	Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
119	139	Phobius	TRANSMEMBRANE	Region of a membrane-bound protein predicted to be embedded in the membrane.
215	237	Phobius	TRANSMEMBRANE	Region of a membrane-bound protein predicted to be embedded in the membrane.
373	392	TMHMM	TMhelix	Region of a membrane-bound protein predicted to be embedded in the membrane.
154	174	Phobius	TRANSMEMBRANE	Region of a membrane-bound protein predicted to be embedded in the membrane.
370	388	PRINTS	PR00303	Preprotein translocase SecY subunit signature
180	203	PRINTS	PR00303	Preprotein translocase SecY subunit signature
272	291	PRINTS	PR00303	Preprotein translocase SecY subunit signature
315	337	PRINTS	PR00303	Preprotein translocase SecY subunit signature
402	420	PRINTS	PR00303	Preprotein translocase SecY subunit signature
154	179	PRINTS	PR00303	Preprotein translocase SecY subunit signature
23	41	PRINTS	PR00303	Preprotein translocase SecY subunit signature
75	95	PRINTS	PR00303	Preprotein translocase SecY subunit signature
116	139	PRINTS	PR00303	Preprotein translocase SecY subunit signature
18	422	PANTHER	PTHR10906	SECY/SEC61-ALPHA FAMILY MEMBER
18	422	InterPro	IPR002208	SecY/SEC61-alpha family
297	315	Phobius	NON_CYTOPLASMIC_DOMAIN	Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
173	190	ProSitePatterns	PS00756	Protein secY signature 2.
173	190	InterPro	IPR030659	SecY conserved site
119	138	TMHMM	TMhelix	Region of a membrane-bound protein predicted to be embedded in the membrane.

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_A0A0H3GZ91	AlphaFold	—	—	full sequence	—	Viewing
ColabFold KP13_00769	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
44				0.924
25				0.484
3				0.204

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	18.88	0.831
2	10.59	0.569
3	8.72	0.466
4	8.43	0.449
5	7.37	0.385

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
13				0.928
1				0.647

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	19.45	0.839
2	14.87	0.737
3	10.33	0.555
4	9.28	0.498
5	8.65	0.463

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.

53 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
BEF	5EUL	A4IJK8	66.0 Da LogP 0.88 TPSA 0.0	✓ Ro5	✓ Clean	`[Be-](F)(F)F`
OLC	5AWW	Q5SHQ8	356.5 Da LogP 4.92 TPSA 66.8	✓ Ro5	✓ Clean	`CCCCCCCC\C=C/CCCCCCCC(=O)OC[C@@H](CO)O`
PGV	6ITC	A4IJK8	749.0 Da LogP 10.45 TPSA 148.8	2 viol.	✓ Clean	`CCCCCCCCCCCCCCCC(=O)OC[C@H](CO[P@](=O)(O)OC[C@H…`

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
ZINC32840902	1.000	356.5 Da LogP 4.92 TPSA 66.8	✓ Ro5	✓ Clean	`CCCCCCCC/C=C/CCCCCCCC(=O)OC[C@@H](O)CO`
ZINC32840903	1.000	356.5 Da LogP 4.92 TPSA 66.8	✓ Ro5	✓ Clean	`CCCCCCCC/C=C\CCCCCCCC(=O)OC[C@H](O)CO`
ZINC32840904	1.000	356.5 Da LogP 4.92 TPSA 66.8	✓ Ro5	✓ Clean	`CCCCCCCC/C=C/CCCCCCCC(=O)OC[C@H](O)CO`
ZINC102191119	0.875	498.6 Da LogP 3.65 TPSA 148.8	✓ Ro5	✓ Clean	`CCCCCCCC(=O)OC[C@H](CO[P@@](=O)(O)OC[C@@H](O)CO…`
ZINC58649551	0.875	498.6 Da LogP 3.65 TPSA 148.8	✓ Ro5	✓ Clean	`CCCCCCCC(=O)OC[C@H](CO[P@@](=O)(O)OC[C@H](O)CO)…`
ZINC102191158	0.700	456.5 Da LogP 3.08 TPSA 142.8	✓ Ro5	✓ Clean	`CCCCCCCCCCCCCC(=O)OC[C@H](O)CO[P@@](=O)(O)OC[C@…`
ZINC14880758	0.700	484.6 Da LogP 3.86 TPSA 142.8	✓ Ro5	✓ Clean	`CCCCCCCCCCCCCCCC(=O)OC[C@@H](O)CO[P@](=O)(O)OC[…`
ZINC14880760	0.700	484.6 Da LogP 3.86 TPSA 142.8	✓ Ro5	✓ Clean	`CCCCCCCCCCCCCCCC(=O)OC[C@H](O)CO[P@](=O)(O)OC[C…`
ZINC53683910	0.700	484.6 Da LogP 3.86 TPSA 142.8	✓ Ro5	✓ Clean	`CCCCCCCCCCCCCCCC(=O)OC[C@H](O)CO[P@@](=O)(O)OC[…`
ZINC62592202	0.700	456.5 Da LogP 3.08 TPSA 142.8	✓ Ro5	✓ Clean	`CCCCCCCCCCCCCC(=O)OC[C@H](O)CO[P@@](=O)(O)OC[C@…`
ZINC62592203	0.700	456.5 Da LogP 3.08 TPSA 142.8	✓ Ro5	✓ Clean	`CCCCCCCCCCCCCC(=O)OC[C@@H](O)CO[P@@](=O)(O)OC[C…`
ZINC62592204	0.700	484.6 Da LogP 3.86 TPSA 142.8	✓ Ro5	✓ Clean	`CCCCCCCCCCCCCCCC(=O)OC[C@@H](O)CO[P@@](=O)(O)OC…`
ZINC96094841	0.700	456.5 Da LogP 3.08 TPSA 142.8	✓ Ro5	✓ Clean	`CCCCCCCCCCCCCC(=O)OC[C@@H](O)CO[P@@](=O)(O)OC[C…`
ZINC1501016272	0.673	328.5 Da LogP 4.14 TPSA 66.8	✓ Ro5	✓ Clean	`CCCCCCC/C=C\CCCCCCC(=O)OC[C@H](O)CO`
ZINC1501016273	0.673	328.5 Da LogP 4.14 TPSA 66.8	✓ Ro5	✓ Clean	`CCCCCCC/C=C\CCCCCCC(=O)OC[C@@H](O)CO`
ZINC1501016315	0.673	314.5 Da LogP 3.75 TPSA 66.8	✓ Ro5	✓ Clean	`CCCCCC/C=C\CCCCCCC(=O)OC[C@@H](O)CO`
ZINC1501016316	0.673	314.5 Da LogP 3.75 TPSA 66.8	✓ Ro5	✓ Clean	`CCCCCC/C=C\CCCCCCC(=O)OC[C@H](O)CO`
ZINC2038077522	0.673	356.5 Da LogP 4.92 TPSA 66.8	✓ Ro5	✓ Clean	`CCCCCCCCC=CCCCCCCCC(=O)OC[C@@H](O)CO`
ZINC2038077523	0.673	356.5 Da LogP 4.92 TPSA 66.8	✓ Ro5	✓ Clean	`CCCCCCCCC=CCCCCCCCC(=O)OC[C@H](O)CO`
ZINC221534416	0.673	328.5 Da LogP 4.14 TPSA 66.8	✓ Ro5	✓ Clean	`CCCCCCCC/C=C\CCCCCC(=O)OC[C@@H](O)CO`
ZINC32840893	0.673	328.5 Da LogP 4.14 TPSA 66.8	✓ Ro5	✓ Clean	`CCCCCC/C=C\CCCCCCCC(=O)OC[C@@H](O)CO`
ZINC32840894	0.673	328.5 Da LogP 4.14 TPSA 66.8	✓ Ro5	✓ Clean	`CCCCCC/C=C/CCCCCCCC(=O)OC[C@@H](O)CO`
ZINC32840895	0.673	328.5 Da LogP 4.14 TPSA 66.8	✓ Ro5	✓ Clean	`CCCCCC/C=C\CCCCCCCC(=O)OC[C@H](O)CO`
ZINC32840896	0.673	328.5 Da LogP 4.14 TPSA 66.8	✓ Ro5	✓ Clean	`CCCCCC/C=C/CCCCCCCC(=O)OC[C@H](O)CO`
ZINC32840901	0.673	356.5 Da LogP 4.92 TPSA 66.8	✓ Ro5	✓ Clean	`CCCCCCCC/C=C\CCCCCCCC(=O)OC[C@@H](O)CO`
ZINC725433050	0.673	342.5 Da LogP 4.53 TPSA 66.8	✓ Ro5	✓ Clean	`CCCCCCCC/C=C\CCCCCCC(=O)OC[C@@H](O)CO`
ZINC725433052	0.673	342.5 Da LogP 4.53 TPSA 66.8	✓ Ro5	✓ Clean	`CCCCCCCC/C=C\CCCCCCC(=O)OC[C@H](O)CO`
ZINC98208566	0.673	328.5 Da LogP 4.14 TPSA 66.8	✓ Ro5	✓ Clean	`CCCCCCCC/C=C\CCCCCC(=O)OC[C@H](O)CO`
ZINC1501016364	0.661	465.6 Da LogP 4.63 TPSA 128.3	✓ Ro5	✓ Clean	`CCCCCC/C=C\CCCCCCCCC(=O)OC[C@@H](O)CO[P@](=O)(O…`
ZINC102190506	0.648	467.5 Da LogP 4.25 TPSA 134.4	✓ Ro5	✓ Clean	`CCCCCCCC(=O)OC[C@H](CO[P@@](=O)(O)OCCN)OC(=O)CC…`
ZINC102190512	0.648	467.5 Da LogP 4.25 TPSA 134.4	✓ Ro5	✓ Clean	`CCCCCCCC(=O)OC[C@@H](CO[P@@](=O)(O)OCCN)OC(=O)C…`
ZINC144389541	0.642	422.5 Da LogP 4.65 TPSA 113.3	✓ Ro5	✓ Clean	`CCCCCC/C=C\CCCCCCCCC(=O)OC[C@@H](O)COP(=O)(O)O`
ZINC32840885	0.640	300.4 Da LogP 3.36 TPSA 66.8	✓ Ro5	✓ Clean	`CCCC/C=C\CCCCCCCC(=O)OC[C@@H](O)CO`
ZINC2053467566	0.635	354.5 Da LogP 4.70 TPSA 66.8	✓ Ro5	✓ Clean	`CCCCCC=CCC=CCCCCCCCC(=O)OC[C@@H](O)CO`
ZINC2053467567	0.635	354.5 Da LogP 4.70 TPSA 66.8	✓ Ro5	✓ Clean	`CCCCCC=CCC=CCCCCCCCC(=O)OC[C@H](O)CO`
ZINC29045599	0.635	354.5 Da LogP 4.70 TPSA 66.8	✓ Ro5	✓ Clean	`CCCCC/C=C/C/C=C\CCCCCCCC(=O)OC[C@H](O)CO`
ZINC4557100	0.635	354.5 Da LogP 4.70 TPSA 66.8	✓ Ro5	✓ Clean	`CCCCC/C=C\C/C=C\CCCCCCCC(=O)OC[C@H](O)CO`
ZINC4557101	0.635	354.5 Da LogP 4.70 TPSA 66.8	✓ Ro5	✓ Clean	`CCCCC/C=C\C/C=C\CCCCCCCC(=O)OC[C@@H](O)CO`
ZINC5819989	0.635	354.5 Da LogP 4.70 TPSA 66.8	✓ Ro5	✓ Clean	`CCCCC/C=C/C/C=C/CCCCCCCC(=O)OC[C@H](O)CO`
ZINC5819990	0.635	354.5 Da LogP 4.70 TPSA 66.8	✓ Ro5	✓ Clean	`CCCCC/C=C/C/C=C/CCCCCCCC(=O)OC[C@@H](O)CO`
ZINC85425978	0.635	354.5 Da LogP 4.70 TPSA 66.8	✓ Ro5	✓ Clean	`CCCCC/C=C\C/C=C/CCCCCCCC(=O)OC[C@H](O)CO`
ZINC36178999	0.627	424.5 Da LogP 4.27 TPSA 119.4	✓ Ro5	✓ Clean	`CCCCCCCC(=O)OC[C@@H](COP(=O)(O)O)OC(=O)CCCCCCC`
ZINC36179002	0.627	424.5 Da LogP 4.27 TPSA 119.4	✓ Ro5	✓ Clean	`CCCCCCCC(=O)OC[C@H](COP(=O)(O)O)OC(=O)CCCCCCC`
ZINC60153361	0.621	479.6 Da LogP 4.63 TPSA 125.3	✓ Ro5	✓ Clean	`CCCCCCCC/C=C\CCCCCCCC(=O)NCCO[P@@](=O)(O)OC[C@H…`
ZINC60153363	0.621	479.6 Da LogP 4.63 TPSA 125.3	✓ Ro5	✓ Clean	`CCCCCCCC/C=C\CCCCCCCC(=O)NCCO[P@@](=O)(O)OC[C@@…`
ZINC29045446	0.615	352.5 Da LogP 4.47 TPSA 66.8	✓ Ro5	✓ Clean	`CCCCC/C=C\C/C=C\C/C=C\CCCCC(=O)OC[C@@H](O)CO`
ZINC5820131	0.608	368.4 Da LogP 2.71 TPSA 119.4	✓ Ro5	✓ Clean	`CCCCCC(=O)OC[C@@H](COP(=O)(O)O)OC(=O)CCCCC`
ZINC5820134	0.608	368.4 Da LogP 2.71 TPSA 119.4	✓ Ro5	✓ Clean	`CCCCCC(=O)OC[C@H](COP(=O)(O)O)OC(=O)CCCCC`
ZINC13507461	0.607	434.5 Da LogP 4.81 TPSA 113.3	✓ Ro5	✓ Clean	`CCCCC/C=C/C/C=C/CCCCCCCC(=O)OC[C@@H](O)COP(=O)(…`
ZINC5510441	0.607	434.5 Da LogP 4.81 TPSA 113.3	✓ Ro5	✓ Clean	`CCCCC/C=C/C/C=C/CCCCCCCC(=O)OC[C@H](O)COP(=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.