Protein profile

PA5277

diaminopimelate decarboxylase

Genome: NC_002516.2

Gene: PA5277 lysA Structure source: AlphaFold UniProt P19572

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Amino acids 415

Annotations 5

Features 41

PDB binders 11

Druggability 0.668

Overview

Basic information about this protein and its source genome.

Accession: PA5277
Assembly: Pseudomonas aeruginosa PAO1, complete genome
Gene: PA5277 lysA
Status: annotated
Amino acids: 415
Structure source: AlphaFold

4.1.1.20

GO:0008836 Catalysis of the reaction: meso-2,6-diaminopimelate + H+ = L-lysine + CO2. GO:0030170 Binding to pyridoxal 5' phosphate, 3-hydroxy-5-(hydroxymethyl)-2-methyl4-pyridine carboxaldehyde 5' phosphate, the biologically active form of vitamin B6. GO:0009089 OBSOLETE. The chemical reactions and pathways resulting in the formation of lysine, via the intermediate diaminopimelate. GO:0003824 Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.

Target profile

Computed evidence for target prioritization.

Human off-target: hit
Human identity (%): 31.646
Human E-value: 4.39e-06
Gut microbiome off-target: hit
Essential (DEG): Y
Localization: Cytoplasmic

Selected Druggability evidence

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 0.668

Structure –

Pocket –

Sequence

Primary amino-acid sequence viewer.

MDTFSYRDAELFAEGVALSRIAERFGTPTYVYSRAHIEAQYRAYADALAGMPHLVCFAVKANSNLGVLNVLARLGAGFDIVSRGELERVLAAGGDPAKVVFSGVGKTRDDMRRALEVGVHCFNVESGEELERLQRVAAELGVKAPVSLRVNPDVDAQTHPYISTGLKENKFGIAIDEAEAVYARAAELDHLEVIGVDCHIGSQLTQLEPFLDALERLLGLVDRLAGKGIGIRHLDLGGGLGVRYRDEQPPLAGDYIRAIRERLHGRDLTLVFEPGRSIVANAGVLLTRVEYLKHTEHKDFAIVDAAMNDLIRPALYQAWMDVQAVRPRDAAPRRYDLVGPICETGDFLAKDRDLALAEGDLLAVRSAGAYGFVMSSNYNTRGRAAEVLVDGEQTHEVRRRETVQELYAGESLLPQ

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 4 GO

Enzyme Commission (EC)

4.1.1.20

Gene Ontology (GO)

GO:0008836 Catalysis of the reaction: meso-2,6-diaminopimelate + H+ = L-lysine + CO2.
GO:0030170 Binding to pyridoxal 5' phosphate, 3-hydroxy-5-(hydroxymethyl)-2-methyl4-pyridine carboxaldehyde 5' phosphate, the biologically active form of vitamin B6.
GO:0009089 OBSOLETE. The chemical reactions and pathways resulting in the formation of lysine, via the intermediate diaminopimelate.
GO:0003824 Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.

Sequence Features

Domain/signature hits from InterPro and related databases.

41 records

Show feature table

Start	End	DB	Term	Name
16	407	Gene3D	G3DSA:2.40.37.10	Lyase, Ornithine Decarboxylase; Chain A, domain 1
16	407	InterPro	IPR009006	Alanine racemase/group IV decarboxylase, C-terminal
34	277	FunFam	G3DSA:3.20.20.10:FF:000003	Diaminopimelate decarboxylase
15	411	Hamap	MF_02120	Diaminopimelate decarboxylase [lysA].
15	411	InterPro	IPR002986	Diaminopimelate decarboxylase, LysA
281	368	Pfam	PF00278	Pyridoxal-dependent decarboxylase, C-terminal sheet domain
281	368	InterPro	IPR022643	Orn/DAP/Arg decarboxylase 2, C-terminal
268	407	FunFam	G3DSA:2.40.37.10:FF:000003	Diaminopimelate decarboxylase
26	282	SUPERFAMILY	SSF51419	PLP-binding barrel
26	282	InterPro	IPR029066	PLP-binding barrel
35	280	Pfam	PF02784	Pyridoxal-dependent decarboxylase, pyridoxal binding domain
35	280	InterPro	IPR022644	Orn/DAP/Arg decarboxylase 2, N-terminal
57	75	ProSitePatterns	PS00878	Orn/DAP/Arg decarboxylases family 2 pyridoxal-P attachment site.
57	75	InterPro	IPR022653	Orn/DAP/Arg decarboxylase 2, pyridoxal-phosphate binding site
164	173	PRINTS	PR01181	Diaminopimelate decarboxylase signature
164	173	InterPro	IPR002986	Diaminopimelate decarboxylase, LysA
298	316	PRINTS	PR01181	Diaminopimelate decarboxylase signature
298	316	InterPro	IPR002986	Diaminopimelate decarboxylase, LysA
75	92	PRINTS	PR01181	Diaminopimelate decarboxylase signature
75	92	InterPro	IPR002986	Diaminopimelate decarboxylase, LysA
378	400	PRINTS	PR01181	Diaminopimelate decarboxylase signature
378	400	InterPro	IPR002986	Diaminopimelate decarboxylase, LysA
255	411	SUPERFAMILY	SSF50621	Alanine racemase C-terminal domain-like
255	411	InterPro	IPR009006	Alanine racemase/group IV decarboxylase, C-terminal
25	389	CDD	cd06828	PLPDE_III_DapDC
25	389	InterPro	IPR002986	Diaminopimelate decarboxylase, LysA
34	277	Gene3D	G3DSA:3.20.20.10	Alanine racemase
34	277	InterPro	IPR029066	PLP-binding barrel
6	410	NCBIfam	TIGR01048	diaminopimelate decarboxylase
6	410	InterPro	IPR002986	Diaminopimelate decarboxylase, LysA
57	75	PRINTS	PR01179	Ornithine/diaminopimelate/arginine (ODA) decarboxylase family signature
57	75	InterPro	IPR000183	Ornithine/DAP/Arg decarboxylase
368	381	PRINTS	PR01179	Ornithine/diaminopimelate/arginine (ODA) decarboxylase family signature
368	381	InterPro	IPR000183	Ornithine/DAP/Arg decarboxylase
190	203	PRINTS	PR01179	Ornithine/diaminopimelate/arginine (ODA) decarboxylase family signature
190	203	InterPro	IPR000183	Ornithine/DAP/Arg decarboxylase
270	289	PRINTS	PR01179	Ornithine/diaminopimelate/arginine (ODA) decarboxylase family signature
270	289	InterPro	IPR000183	Ornithine/DAP/Arg decarboxylase
77	89	PRINTS	PR01179	Ornithine/diaminopimelate/arginine (ODA) decarboxylase family signature
77	89	InterPro	IPR000183	Ornithine/DAP/Arg decarboxylase
6	407	PANTHER	PTHR43727	DIAMINOPIMELATE DECARBOXYLASE

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 + 1

Experimental PDB entries and predicted models. Click Switch to display a different structure in the viewer.

Entry	Method	Resolution	Chain	Coverage	Links	Status
AlphaFold PA5277	AlphaFold	—	—	full sequence	—	Viewing

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
7				0.668
3				0.509
5				0.378

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
AZ1	1TUF	Q58497	188.2 Da LogP 1.89 TPSA 74.6	✓ Ro5	✓ Clean	`C(CCCC(=O)O)CCCC(=O)O`
DMO	2TOD	P07805	182.2 Da LogP -0.23 TPSA 89.3	✓ Ro5	✓ Clean	`C(CC(C(F)F)(C(=O)O)N)CN`
DN9	6KNK	A0A0H3JPF2	465.4 Da LogP -1.41 TPSA 235.8	1 viol.	✓ Clean	`Cc1c(c(c(cn1)COP(=O)(O)O)CNCCNC(=O)C[C@](CC(=O)…`
GET	1NJJ	Q9TZZ6	496.6 Da LogP -5.61 TPSA 248.4	2 viol.	✓ Clean	`C[C@H]([C@@H]1[C@H]([C@@H]([C@H]([C@H](O1)O[C@@…`
LLP	4XG1	A1SR00	375.3 Da LogP 0.71 TPSA 175.6	✓ Ro5	✓ Clean	`Cc1c(c(c(cn1)COP(=O)(O)O)/C=N/CCCCC(C(=O)O)N)O`
ORX	1SZR	P07805	363.3 Da LogP -0.01 TPSA 175.2	1 viol.	✓ Clean	`Cc1c(c(c(cn1)COP(=O)(O)O)CN[C@H](CCCN)C(=O)O)O`
PLG	1SZR	P07805	306.2 Da LogP -0.12 TPSA 149.2	✓ Ro5	✓ Clean	`Cc1c(c(c(cn1)COP(=O)(O)O)CNCC(=O)O)O`
PUT	1F3T	P07805	88.2 Da LogP -0.32 TPSA 52.0	✓ Ro5	✓ Clean	`C(CCN)CN`
PXP	1SZR	P07805	249.2 Da LogP 0.20 TPSA 120.1	✓ Ro5	✓ Clean	`Cc1c(c(c(cn1)COP(=O)(O)O)CO)O`
TME	4XG1	A1SR00	44.1 Da LogP 1.42 TPSA 0.0	✓ Ro5	✓ Clean	`CCC`
X3J	6KNK	A0A0H3JPF2	234.2 Da LogP -2.26 TPSA 150.0	✓ Ro5	✓ Clean	`C(CNC(=O)C[C@](CC(=O)O)(C(=O)O)O)N`

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
ZINC100069123	1.000	496.6 Da LogP -5.61 TPSA 248.4	2 viol.	✓ Clean	`CN[C@H]1[C@H](O)[C@H](O[C@@H]2[C@@H](O)[C@H](O[…`
ZINC106588639	1.000	496.6 Da LogP -5.61 TPSA 248.4	2 viol.	✓ Clean	`CN[C@H]1[C@H](O)[C@H](O[C@@H]2[C@@H](N)C[C@@H](…`
ZINC1772820029	1.000	496.6 Da LogP -5.61 TPSA 248.4	2 viol.	✓ Clean	`CN[C@@H]1[C@@H](O)[C@@H](O[C@@H]2[C@@H](O)[C@H]…`
ZINC1857790211	1.000	496.6 Da LogP -5.61 TPSA 248.4	2 viol.	✓ Clean	`CN[C@@H]1[C@@H](O)[C@@H](O[C@@H]2[C@@H](N)C[C@@…`
ZINC1857790212	1.000	496.6 Da LogP -5.61 TPSA 248.4	2 viol.	✓ Clean	`CN[C@@H]1[C@@H](O)[C@@H](O[C@@H]2[C@@H](N)C[C@@…`
ZINC252460108	1.000	496.6 Da LogP -5.61 TPSA 248.4	2 viol.	✓ Clean	`CN[C@H]1[C@H](O)[C@H](O[C@@H]2[C@@H](N)C[C@@H](…`
ZINC253380792	1.000	496.6 Da LogP -5.61 TPSA 248.4	2 viol.	✓ Clean	`CN[C@@H]1[C@H](O)[C@H](O[C@@H]2[C@H](N)C[C@H](N…`
ZINC253380793	1.000	496.6 Da LogP -5.61 TPSA 248.4	2 viol.	✓ Clean	`CN[C@@H]1[C@H](O)[C@H](O[C@@H]2[C@H](N)C[C@H](N…`
ZINC253380794	1.000	496.6 Da LogP -5.61 TPSA 248.4	2 viol.	✓ Clean	`CN[C@@H]1[C@H](O)[C@H](O[C@H]2[C@@H](O)[C@@H](O…`
ZINC253380795	1.000	496.6 Da LogP -5.61 TPSA 248.4	2 viol.	✓ Clean	`CN[C@@H]1[C@H](O)[C@H](O[C@H]2[C@@H](O)[C@@H](O…`
ZINC43543817	1.000	496.6 Da LogP -5.61 TPSA 248.4	2 viol.	✓ Clean	`CN[C@@H]1[C@@H](O)[C@@H](O[C@@H]2[C@@H](O)[C@H]…`
ZINC49708768	1.000	496.6 Da LogP -5.61 TPSA 248.4	2 viol.	✓ Clean	`CN[C@@H]1[C@@H](O)[C@@H](O[C@@H]2[C@@H](O)[C@H]…`
ZINC60183639	1.000	496.6 Da LogP -5.61 TPSA 248.4	2 viol.	✓ Clean	`CN[C@H]1[C@@H](O)[C@@H](O[C@H]2[C@@H](N)C[C@@H]…`
ZINC60183641	1.000	496.6 Da LogP -5.61 TPSA 248.4	2 viol.	✓ Clean	`CN[C@H]1[C@@H](O)[C@@H](O[C@H]2[C@@H](N)C[C@@H]…`
ZINC60183644	1.000	496.6 Da LogP -5.61 TPSA 248.4	2 viol.	✓ Clean	`CN[C@H]1[C@@H](O)[C@@H](O[C@H]2[C@@H](N)C[C@@H]…`
ZINC60183647	1.000	496.6 Da LogP -5.61 TPSA 248.4	2 viol.	✓ Clean	`CN[C@H]1[C@@H](O)[C@@H](O[C@H]2[C@@H](N)C[C@@H]…`
ZINC60184326	1.000	496.6 Da LogP -5.61 TPSA 248.4	2 viol.	✓ Clean	`CN[C@H]1[C@H](O)[C@H](O[C@@H]2[C@@H](O)[C@H](O[…`
ZINC64857811	1.000	496.6 Da LogP -5.61 TPSA 248.4	2 viol.	✓ Clean	`CN[C@H]1[C@@H](O)[C@@H](O[C@@H]2[C@@H](O)[C@H](…`
ZINC70691602	1.000	496.6 Da LogP -5.61 TPSA 248.4	2 viol.	✓ Clean	`CN[C@H]1[C@H](O)[C@@H](O[C@@H]2[C@@H](N)C[C@@H]…`
ZINC70691603	1.000	496.6 Da LogP -5.61 TPSA 248.4	2 viol.	✓ Clean	`CN[C@H]1[C@H](O)[C@@H](O[C@@H]2[C@@H](N)C[C@@H]…`
ZINC70691604	1.000	496.6 Da LogP -5.61 TPSA 248.4	2 viol.	✓ Clean	`CN[C@H]1[C@H](O)[C@H](O[C@@H]2[C@@H](N)C[C@@H](…`
ZINC70691605	1.000	496.6 Da LogP -5.61 TPSA 248.4	2 viol.	✓ Clean	`CN[C@H]1[C@H](O)[C@H](O[C@@H]2[C@@H](N)C[C@@H](…`
ZINC72332859	1.000	496.6 Da LogP -5.61 TPSA 248.4	2 viol.	✓ Clean	`CN[C@H]1[C@H](O)[C@@H](O[C@@H]2[C@@H](N)C[C@@H]…`
ZINC72332860	1.000	496.6 Da LogP -5.61 TPSA 248.4	2 viol.	✓ Clean	`CN[C@H]1[C@H](O)[C@@H](O[C@@H]2[C@@H](N)C[C@@H]…`
ZINC936069019	1.000	496.6 Da LogP -5.61 TPSA 248.4	2 viol.	✓ Clean	`CN[C@@H]1[C@H](O)[C@@H](O[C@@H]2[C@H](N)C[C@H](…`
ZINC936069020	1.000	496.6 Da LogP -5.61 TPSA 248.4	2 viol.	✓ Clean	`CN[C@@H]1[C@H](O)[C@@H](O[C@@H]2[C@H](N)C[C@H](…`
ZINC936069021	1.000	496.6 Da LogP -5.61 TPSA 248.4	2 viol.	✓ Clean	`CN[C@@H]1[C@H](O)[C@@H](O[C@@H]2[C@H](N)C[C@H](…`
ZINC936069022	1.000	496.6 Da LogP -5.61 TPSA 248.4	2 viol.	✓ Clean	`CN[C@@H]1[C@H](O)[C@@H](O[C@@H]2[C@H](N)C[C@H](…`
ZINC1685531	0.875	200.4 Da LogP 2.80 TPSA 52.0	✓ Ro5	✓ Clean	`NCCCCCCCCCCCCN`
ZINC34273707	0.875	256.5 Da LogP 4.37 TPSA 52.0	✓ Ro5	✓ Clean	`NCCCCCCCCCCCCCCCCN`
ZINC5178646	0.875	228.4 Da LogP 3.59 TPSA 52.0	✓ Ro5	✓ Clean	`NCCCCCCCCCCCCCCN`
ZINC14686440	0.759	436.4 Da LogP -2.64 TPSA 247.9	1 viol.	✓ Clean	`O=C(O)C[C@](O)(CC(=O)NCCCCNC(=O)C[C@@](O)(CC(=O…`
ZINC14686442	0.759	436.4 Da LogP -2.64 TPSA 247.9	1 viol.	✓ Clean	`O=C(O)C[C@@](O)(CC(=O)NCCCCNC(=O)C[C@](O)(CC(=O…`
ZINC14686444	0.759	436.4 Da LogP -2.64 TPSA 247.9	1 viol.	✓ Clean	`O=C(O)C[C@@](O)(CC(=O)NCCCCNC(=O)C[C@@](O)(CC(=…`
ZINC13433578	0.750	201.3 Da LogP 1.68 TPSA 80.4	✓ Ro5	✓ Clean	`NC(=O)CCCCCCCCC(=O)O`
ZINC14510370	0.750	244.4 Da LogP 3.74 TPSA 57.5	✓ Ro5	✓ Clean	`O=C(O)CCCCCCCCCCCCCO`
ZINC1531061	0.750	216.3 Da LogP 2.96 TPSA 57.5	✓ Ro5	✓ Clean	`O=C(O)CCCCCCCCCCCO`
ZINC1610426	0.750	230.3 Da LogP 3.35 TPSA 57.5	✓ Ro5	✓ Clean	`O=C(O)CCCCCCCCCCCCO`
ZINC2168567	0.750	202.3 Da LogP 2.57 TPSA 57.5	✓ Ro5	✓ Clean	`O=C(O)CCCCCCCCCCO`
ZINC3074815	0.750	230.3 Da LogP 1.85 TPSA 91.7	✓ Ro5	✓ Clean	`O=C(O)CCCCCC(=O)CCCC(=O)O`
ZINC3861297	0.750	272.4 Da LogP 4.52 TPSA 57.5	✓ Ro5	✓ Clean	`O=C(O)CCCCCCCCCCCCCCCO`
ZINC4284502	0.750	258.4 Da LogP 4.13 TPSA 57.5	✓ Ro5	✓ Clean	`O=C(O)CCCCCCCCCCCCCCO`
ZINC5287109	0.750	286.5 Da LogP 4.91 TPSA 57.5	✓ Ro5	✓ Clean	`O=C(O)CCCCCCCCCCCCCCCCO`
ZINC2382315402	0.707	481.5 Da LogP -6.04 TPSA 254.2	2 viol.	✓ Clean	`CN[C@@H]1[C@H](O)[C@H](O[C@@H]2[C@@H](N)C[C@H](…`
ZINC138216182	0.706	293.2 Da LogP 4.76 TPSA 37.3	✓ Ro5	✓ Clean	`O=C(O)CCCCCCCCCCCCBr`
ZINC1529498	0.706	200.3 Da LogP 3.99 TPSA 37.3	✓ Ro5	✓ Clean	`CCCCCCCCCCCC(=O)O`
ZINC1841307	0.706	228.3 Da LogP 3.56 TPSA 54.4	✓ Ro5	✓ Clean	`CC(=O)CCCCCCCCCCC(=O)O`
ZINC1845839	0.706	200.3 Da LogP 2.78 TPSA 54.4	✓ Ro5	✓ Clean	`CC(=O)CCCCCCCCC(=O)O`
ZINC33822328	0.706	270.4 Da LogP 4.73 TPSA 54.4	✓ Ro5	✓ Clean	`CC(=O)CCCCCCCCCCCCCC(=O)O`
ZINC35465466	0.706	244.3 Da LogP 2.24 TPSA 91.7	✓ Ro5	✓ Clean	`O=C(O)CCCCCCCC(=O)CCC(=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.