Protein profile

KP13_00519

Phosphatidylserine decarboxylase proenzyme

Genome: KpKP13

Gene: AHE46747.1 psd Structure source: AlphaFold + ColabFold UniProt A0A0H3GM92

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Amino acids 320

Annotations 5

Features 10

PDB binders 3

Druggability 0.797

Overview

Basic information about this protein and its source genome.

Accession: KP13_00519
Assembly: Klebsiella pneumoniae subsp. pneumoniae Kp13, complete sequence
Gene: AHE46747.1 psd
Status: annotated
Amino acids: 320
Structure source: AlphaFold + ColabFold

4.1.1.65

GO:0004609 Catalysis of the reaction: H+ + phosphatidyl-L-serine = CO2 + phosphatidylethanolamine. GO:0008654 The chemical reactions and pathways resulting in the formation of a phospholipid, a lipid containing phosphoric acid as a mono- or diester. 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:0006646 The chemical reactions and pathways resulting in the formation of phosphatidylethanolamine, any of a class of glycerophospholipids in which a phosphatidyl group is esterified to the hydroxyl group of ethanolamine.

Target profile

Computed evidence for target prioritization.

Human off-target: hit
Human identity (%): 36.458
Human E-value: 4.32e-12
Gut microbiome off-target: hit
Essential (DEG): Y
DEG identity (%): 88.785
DEG E-value: 0.0
Localization: CytoplasmicMembrane
ColabFold pLDDT: 89.96

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 0.797

Structure A0A0H3GM92

Pocket Pocket 9

P2Rank 0.534

Structure A0A0H3GM92

Pocket Pocket 1

ColabFold model

FPocket 0.949 · Pocket 4

P2Rank 0.326 · Pocket 1

Core conservation Conserved core gene

Roary core

CoreCruncher core

Gut microbiome 167 / 4744 genomes with a hit

Normalized 0.035

Sequence

Primary amino-acid sequence viewer.

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 4 GO

Enzyme Commission (EC)

4.1.1.65

Gene Ontology (GO)

GO:0004609 Catalysis of the reaction: H+ + phosphatidyl-L-serine = CO2 + phosphatidylethanolamine.
GO:0008654 The chemical reactions and pathways resulting in the formation of a phospholipid, a lipid containing phosphoric acid as a mono- or diester.
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:0006646 The chemical reactions and pathways resulting in the formation of phosphatidylethanolamine, any of a class of glycerophospholipids in which a phosphatidyl group is esterified to the hydroxyl group of ethanolamine.

Sequence Features

Domain/signature hits from InterPro and related databases.

10 records

Show feature table

Start	End	DB	Term	Name
49	285	NCBIfam	TIGR00163	archaetidylserine decarboxylase
49	285	InterPro	IPR033177	Phosphatidylserine decarboxylase, bacterial/eukaryotic
14	287	PANTHER	PTHR10067	PHOSPHATIDYLSERINE DECARBOXYLASE
14	287	InterPro	IPR003817	Phosphatidylserine decarboxylase-related
290	320	MobiDBLite	mobidb-lite	consensus disorder prediction
10	287	Hamap	MF_00662	Phosphatidylserine decarboxylase proenzyme [psd].
10	287	InterPro	IPR033178	Phosphatidylserine decarboxylase, prokaryotic type 1
299	320	MobiDBLite	mobidb-lite	consensus disorder prediction
63	284	Pfam	PF02666	Phosphatidylserine decarboxylase
63	284	InterPro	IPR003817	Phosphatidylserine decarboxylase-related

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_A0A0H3GM92	AlphaFold	—	—	full sequence	—	Viewing
ColabFold KP13_00519	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
9				0.797

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	10.04	0.54
2	2.67	0.079
3	2.12	0.049

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
4				0.949

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	6.62	0.336
2	2.84	0.089
3	2.22	0.054
4	1.97	0.042

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
PEE	6L07	P0A8K1	744.0 Da LogP 11.61 TPSA 134.4	2 viol.	✓ Clean	`CCCCCCCC/C=C\CCCCCCCC(=O)OC[C@H](COP(=O)(O)OCCN…`
PPI	6L07	P0A8K1	74.1 Da LogP 0.48 TPSA 37.3	✓ Ro5	✓ Clean	`CCC(=O)O`
PYR	6L07	P0A8K1	88.1 Da LogP -0.34 TPSA 54.4	✓ Ro5	✓ Clean	`CC(=O)C(=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
ZINC102190506	0.872	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	0.872	467.5 Da LogP 4.25 TPSA 134.4	✓ Ro5	✓ Clean	`CCCCCCCC(=O)OC[C@@H](CO[P@@](=O)(O)OCCN)OC(=O)C…`
ZINC27416437	0.851	411.4 Da LogP 2.69 TPSA 134.4	✓ Ro5	✓ Clean	`CCCCCC(=O)OC[C@H](CO[P@](=O)(O)OCCN)OC(=O)CCCCC`
ZINC33902364	0.851	411.4 Da LogP 2.69 TPSA 134.4	✓ Ro5	✓ Clean	`CCCCCC(=O)OC[C@@H](CO[P@@](=O)(O)OCCN)OC(=O)CCC…`
ZINC1501016364	0.769	465.6 Da LogP 4.63 TPSA 128.3	✓ Ro5	✓ Clean	`CCCCCC/C=C\CCCCCCCCC(=O)OC[C@@H](O)CO[P@](=O)(O…`
ZINC13544781	0.685	482.6 Da LogP 4.22 TPSA 108.4	✓ Ro5	✓ Clean	`CCCCCCC(=O)OC[C@@H](CO[P@](=O)(O)OCC[N+](C)(C)C…`
ZINC13544783	0.685	482.6 Da LogP 4.22 TPSA 108.4	✓ Ro5	✓ Clean	`CCCCCCC(=O)OC[C@H](CO[P@](=O)(O)OCC[N+](C)(C)C)…`
ZINC13543439	0.667	454.5 Da LogP 3.44 TPSA 108.4	✓ Ro5	✓ Clean	`CCCCCC(=O)OC[C@@H](CO[P@](=O)(O)OCC[N+](C)(C)C)…`
ZINC13543441	0.667	454.5 Da LogP 3.44 TPSA 108.4	✓ Ro5	✓ Clean	`CCCCCC(=O)OC[C@H](CO[P@](=O)(O)OCC[N+](C)(C)C)O…`
ZINC102190945	0.654	411.5 Da LogP 3.29 TPSA 128.3	✓ Ro5	✓ Clean	`CCCCCCCCCCCCC(=O)OC[C@@H](O)CO[P@@](=O)(O)OCCN`
ZINC32840692	0.654	425.5 Da LogP 3.68 TPSA 128.3	✓ Ro5	✓ Clean	`CCCCCCCCCCCCCC(=O)OC[C@@H](O)CO[P@](=O)(O)OCCN`
ZINC32840693	0.654	425.5 Da LogP 3.68 TPSA 128.3	✓ Ro5	✓ Clean	`CCCCCCCCCCCCCC(=O)OC[C@H](O)CO[P@](=O)(O)OCCN`
ZINC32840704	0.654	453.6 Da LogP 4.46 TPSA 128.3	✓ Ro5	✓ Clean	`CCCCCCCCCCCCCCCC(=O)OC[C@@H](O)CO[P@](=O)(O)OCCN`
ZINC32840705	0.654	453.6 Da LogP 4.46 TPSA 128.3	✓ Ro5	✓ Clean	`CCCCCCCCCCCCCCCC(=O)OC[C@H](O)CO[P@](=O)(O)OCCN`
ZINC95635984	0.654	397.4 Da LogP 2.90 TPSA 128.3	✓ Ro5	✓ Clean	`CCCCCCCCCCCC(=O)OC[C@@H](O)CO[P@@](=O)(O)OCCN`
ZINC102191119	0.648	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	0.648	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)…`
ZINC36178999	0.640	424.5 Da LogP 4.27 TPSA 119.4	✓ Ro5	✓ Clean	`CCCCCCCC(=O)OC[C@@H](COP(=O)(O)O)OC(=O)CCCCCCC`
ZINC36179002	0.640	424.5 Da LogP 4.27 TPSA 119.4	✓ Ro5	✓ Clean	`CCCCCCCC(=O)OC[C@H](COP(=O)(O)O)OC(=O)CCCCCCC`
ZINC13543394	0.630	455.4 Da LogP 2.15 TPSA 171.7	✓ Ro5	✓ Clean	`CCCCCC(=O)OC[C@H](CO[P@@](=O)(O)OC[C@H](N)C(=O)…`
ZINC5820131	0.620	368.4 Da LogP 2.71 TPSA 119.4	✓ Ro5	✓ Clean	`CCCCCC(=O)OC[C@@H](COP(=O)(O)O)OC(=O)CCCCC`
ZINC5820134	0.620	368.4 Da LogP 2.71 TPSA 119.4	✓ Ro5	✓ Clean	`CCCCCC(=O)OC[C@H](COP(=O)(O)O)OC(=O)CCCCC`
ZINC33822387	0.618	426.5 Da LogP 2.66 TPSA 108.4	✓ Ro5	✓ Clean	`CCCCC(=O)OC[C@H](CO[P@@](=O)(O)OCC[N+](C)(C)C)O…`
ZINC33822389	0.618	426.5 Da LogP 2.66 TPSA 108.4	✓ Ro5	✓ Clean	`CCCCC(=O)OC[C@@H](CO[P@@](=O)(O)OCC[N+](C)(C)C)…`
ZINC144389541	0.564	422.5 Da LogP 4.65 TPSA 113.3	✓ Ro5	✓ Clean	`CCCCCC/C=C\CCCCCCCCC(=O)OC[C@@H](O)COP(=O)(O)O`
ZINC144246453	0.561	422.5 Da LogP 4.02 TPSA 128.0	✓ Ro5	✓ Clean	`CCCCCCCCCCCCC/C=C/[C@@H](O)[C@@H](N)CO[P@@](=O)…`
ZINC12834352	0.554	398.4 Da LogP 1.88 TPSA 108.4	✓ Ro5	✓ Clean	`CCCC(=O)OC[C@@H](CO[P@](=O)(O)OCC[N+](C)(C)C)OC…`
ZINC12834353	0.554	398.4 Da LogP 1.88 TPSA 108.4	✓ Ro5	✓ Clean	`CCCC(=O)OC[C@H](CO[P@](=O)(O)OCC[N+](C)(C)C)OC(…`
ZINC4521879	0.553	386.5 Da LogP 4.73 TPSA 78.9	✓ Ro5	✓ Clean	`CCCCCC(=O)OCC(COC(=O)CCCCC)OC(=O)CCCCC`
ZINC13507461	0.534	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	0.534	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…`
ZINC32840817	0.529	356.5 Da LogP 4.92 TPSA 66.8	✓ Ro5	✓ Clean	`CCCCCCCC/C=C\CCCCCCCC(=O)OC(CO)CO`
ZINC32840818	0.529	356.5 Da LogP 4.92 TPSA 66.8	✓ Ro5	✓ Clean	`CCCCCCCC/C=C/CCCCCCCC(=O)OC(CO)CO`
ZINC36079847	0.510	344.5 Da LogP 4.15 TPSA 72.8	✓ Ro5	✓ Clean	`CCCCCCCC(=O)OC[C@@H](CO)OC(=O)CCCCCCC`
ZINC8214428	0.510	344.5 Da LogP 4.15 TPSA 72.8	✓ Ro5	✓ Clean	`CCCCCCCC(=O)OC[C@H](CO)OC(=O)CCCCCCC`
ZINC13521162	0.509	299.2 Da LogP -0.43 TPSA 134.4	✓ Ro5	✓ Clean	`CC(=O)OC[C@@H](CO[P@](=O)(O)OCCN)OC(C)=O`
ZINC3798545	0.509	299.2 Da LogP -0.43 TPSA 134.4	✓ Ro5	✓ Clean	`CC(=O)OC[C@H](CO[P@@](=O)(O)OCCN)OC(C)=O`
ZINC102189757	0.508	454.6 Da LogP 4.04 TPSA 102.3	✓ Ro5	✓ Clean	`CCCCCCCCCCCCC(=O)OC[C@H](O)CO[P@@](=O)(O)OCC[N+…`
ZINC13544128	0.508	370.4 Da LogP 1.70 TPSA 102.3	✓ Ro5	✓ Clean	`CCCCCCC(=O)OC[C@@H](O)CO[P@](=O)(O)OCC[N+](C)(C…`
ZINC14880038	0.508	440.5 Da LogP 3.65 TPSA 102.3	✓ Ro5	✓ Clean	`CCCCCCCCCCCC(=O)OC[C@@H](O)CO[P@](=O)(O)OCC[N+]…`
ZINC14880039	0.508	440.5 Da LogP 3.65 TPSA 102.3	✓ Ro5	✓ Clean	`CCCCCCCCCCCC(=O)OC[C@H](O)CO[P@@](=O)(O)OCC[N+]…`
ZINC15297567	0.508	468.6 Da LogP 4.43 TPSA 102.3	✓ Ro5	✓ Clean	`CCCCCCCCCCCCCC(=O)OC[C@@H](O)CO[P@@](=O)(O)OCC[…`
ZINC32789157	0.508	412.5 Da LogP 2.87 TPSA 102.3	✓ Ro5	✓ Clean	`CCCCCCCCCC(=O)OC[C@@H](O)CO[P@](=O)(O)OCC[N+](C…`
ZINC32789161	0.508	412.5 Da LogP 2.87 TPSA 102.3	✓ Ro5	✓ Clean	`CCCCCCCCCC(=O)OC[C@H](O)CO[P@](=O)(O)OCC[N+](C)…`
ZINC32822149	0.508	468.6 Da LogP 4.43 TPSA 102.3	✓ Ro5	✓ Clean	`CCCCCCCCCCCCCC(=O)OC[C@H](O)CO[P@](=O)(O)OCC[N+…`
ZINC32822162	0.508	482.6 Da LogP 4.82 TPSA 102.3	✓ Ro5	✓ Clean	`CCCCCCCCCCCCCCC(=O)OC[C@@H](O)CO[P@@](=O)(O)OCC…`
ZINC32822163	0.508	482.6 Da LogP 4.82 TPSA 102.3	✓ Ro5	✓ Clean	`CCCCCCCCCCCCCCC(=O)OC[C@H](O)CO[P@](=O)(O)OCC[N…`
ZINC44305349	0.508	454.6 Da LogP 4.04 TPSA 102.3	✓ Ro5	✓ Clean	`CCCCCCCCCCCCC(=O)OC[C@@H](O)CO[P@@](=O)(O)OCC[N…`
ZINC44405718	0.508	398.5 Da LogP 2.48 TPSA 102.3	✓ Ro5	✓ Clean	`CCCCCCCCC(=O)OC[C@@H](O)CO[P@@](=O)(O)OCC[N+](C…`
ZINC85576534	0.508	384.4 Da LogP 2.09 TPSA 102.3	✓ Ro5	✓ Clean	`CCCCCCCC(=O)OC[C@@H](O)CO[P@@](=O)(O)OCC[N+](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.