Protein profile

PA5243

delta-aminolevulinic acid dehydratase

Genome: NC_002516.2

Gene: PA5243 hemB Structure source: Experimental + AlphaFold UniProt Q59643

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Amino acids 337

Annotations 9

Features 27

PDB binders 4

Druggability 0.671

Overview

Basic information about this protein and its source genome.

Accession: PA5243
Assembly: Pseudomonas aeruginosa PAO1, complete genome
Gene: PA5243 hemB
Status: annotated
Amino acids: 337
Structure source: Experimental + AlphaFold

4.2.1.24

GO:0005829 The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes. GO:0004655 Catalysis of the reaction: 2 5-aminolevulinate = 2 H2O + H+ + porphobilinogen. GO:0008270 Binding to a zinc ion (Zn). GO:0006783 The chemical reactions and pathways resulting in the formation of heme, any compound of iron complexed in a porphyrin (tetrapyrrole) ring, from less complex precursors. GO:0006779 The chemical reactions and pathways resulting in the formation of any member of a large group of derivatives or analogs of porphyrin. Porphyrin consists of a ring of four pyrrole nuclei linked each to the next at their alpha positions through a methine group. GO:0006782 The chemical reactions and pathways resulting in the formation of protoporphyrinogen IX.

Target profile

Computed evidence for target prioritization.

Human off-target: hit
Human identity (%): 43.974
Human E-value: 6.03e-73
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 0.671

Structure –

Pocket –

Sequence

Primary amino-acid sequence viewer.

MSFTPANRAYPYTRLRRNRRDDFSRRLVRENVLTVDDLILPVFVLDGVNQRESIPSMPGVERLSIDQLLIEAEEWVALGIPALALFPVTPVEKKSLDAAEAYNPEGIAQRATRALRERFPELGIITDVALDPFTTHGQDGILDDDGYVLNDVSIDVLVRQALSHAEAGAQVVAPSDMMDGRIGAIREALESAGHTNVRIMAYSAKYASAYYGPFRDAVGSASNLGKGNKATYQMDPANSDEALHEVAADLAEGADMVMVKPGMPYLDIVRRVKDEFRAPTFVYQVSGEYAMHMGAIQNGWLAESVILESLTAFKRAGADGILTYFAKQAAEQLRRGR

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 8 GO

Enzyme Commission (EC)

4.2.1.24

Gene Ontology (GO)

GO:0005829 The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
GO:0004655 Catalysis of the reaction: 2 5-aminolevulinate = 2 H2O + H+ + porphobilinogen.
GO:0008270 Binding to a zinc ion (Zn).
GO:0006783 The chemical reactions and pathways resulting in the formation of heme, any compound of iron complexed in a porphyrin (tetrapyrrole) ring, from less complex precursors.
GO:0006779 The chemical reactions and pathways resulting in the formation of any member of a large group of derivatives or analogs of porphyrin. Porphyrin consists of a ring of four pyrrole nuclei linked each to the next at their alpha positions through a methine group.
GO:0006782 The chemical reactions and pathways resulting in the formation of protoporphyrinogen IX.
GO:0046872 Binding to a metal ion.
GO:0033014 The chemical reactions and pathways leading to the formation of tetrapyrroles, natural pigments containing four pyrrole rings joined by one-carbon units linking position 2 of one pyrrole ring to position 5 of the next.

Sequence Features

Domain/signature hits from InterPro and related databases.

27 records

Show feature table

Start	End	DB	Term	Name
8	334	SUPERFAMILY	SSF51569	Aldolase
8	335	FunFam	G3DSA:3.20.20.70:FF:000019	Delta-aminolevulinic acid dehydratase
13	334	CDD	cd04823	ALAD_PBGS_aspartate_rich
13	331	Pfam	PF00490	Delta-aminolevulinic acid dehydratase
13	331	InterPro	IPR001731	Delta-aminolevulinic acid dehydratase
12	333	PANTHER	PTHR11458	DELTA-AMINOLEVULINIC ACID DEHYDRATASE
12	333	InterPro	IPR001731	Delta-aminolevulinic acid dehydratase
10	333	SMART	SM01004	ALAD_2
10	333	InterPro	IPR001731	Delta-aminolevulinic acid dehydratase
2	336	PIRSF	PIRSF001415	Porphbilin_synth
2	336	InterPro	IPR001731	Delta-aminolevulinic acid dehydratase
1	337	Gene3D	G3DSA:3.20.20.70	Aldolase class I
1	337	InterPro	IPR013785	Aldolase-type TIM barrel
130	144	PRINTS	PR00144	Delta-aminolevulinic acid dehydratase signature
130	144	InterPro	IPR001731	Delta-aminolevulinic acid dehydratase
161	180	PRINTS	PR00144	Delta-aminolevulinic acid dehydratase signature
161	180	InterPro	IPR001731	Delta-aminolevulinic acid dehydratase
307	326	PRINTS	PR00144	Delta-aminolevulinic acid dehydratase signature
307	326	InterPro	IPR001731	Delta-aminolevulinic acid dehydratase
199	218	PRINTS	PR00144	Delta-aminolevulinic acid dehydratase signature
199	218	InterPro	IPR001731	Delta-aminolevulinic acid dehydratase
253	269	PRINTS	PR00144	Delta-aminolevulinic acid dehydratase signature
253	269	InterPro	IPR001731	Delta-aminolevulinic acid dehydratase
278	293	PRINTS	PR00144	Delta-aminolevulinic acid dehydratase signature
278	293	InterPro	IPR001731	Delta-aminolevulinic acid dehydratase
253	265	ProSitePatterns	PS00169	Delta-aminolevulinic acid dehydratase active site.
253	265	InterPro	IPR030656	Delta-aminolevulinic acid dehydratase, active site

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

16 + 1

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

Entry	Method	Resolution	Chain	Coverage	Links	Status
PDB 1W5Q	X-ray	1.40 Å	A,B	100.0% 1-337	PDBe RCSB PDBj File	Viewing
PDB 2C15	X-ray	1.48 Å	A,B	100.0% 1-337	PDBe RCSB PDBj File	Loaded
PDB 1W5P	X-ray	1.55 Å	A,B	100.0% 1-337	PDBe RCSB PDBj File	Loaded
PDB 1W5M	X-ray	1.60 Å	A,B	100.0% 1-337	PDBe RCSB PDBj File	Loaded
PDB 1W5N	X-ray	1.65 Å	A,B	100.0% 1-337	PDBe RCSB PDBj File	Loaded
PDB 1GZG	X-ray	1.66 Å	A,B	100.0% 1-337	PDBe RCSB PDBj File	Loaded
PDB 1B4K	X-ray	1.67 Å	A,B	100.0% 1-337	PDBe RCSB PDBj File	Loaded
PDB 1W56	X-ray	1.70 Å	A,B	100.0% 1-337	PDBe RCSB PDBj File	Loaded
PDB 2WOQ	X-ray	1.75 Å	A	100.0% 1-337	PDBe RCSB PDBj File	Loaded
PDB 1W5O	X-ray	1.85 Å	A,B	100.0% 1-337	PDBe RCSB PDBj File	Loaded
PDB 2C14	X-ray	1.90 Å	A,B	100.0% 1-337	PDBe RCSB PDBj File	Loaded
PDB 2C18	X-ray	1.93 Å	A,B	100.0% 1-337	PDBe RCSB PDBj File	Loaded
PDB 2C16	X-ray	2.02 Å	A,B	100.0% 1-337	PDBe RCSB PDBj File	Loaded
PDB 2C19	X-ray	2.05 Å	A,B	100.0% 1-337	PDBe RCSB PDBj File	Loaded
PDB 2C13	X-ray	2.15 Å	A,B	100.0% 1-337	PDBe RCSB PDBj File	Loaded
PDB 1W54	X-ray	2.20 Å	A,B	100.0% 1-337	PDBe RCSB PDBj File	Loaded
AlphaFold PA5243	AlphaFold	—	—	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				0.671

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	17.19	0.798
2	5.75	0.279
3	4.05	0.163
4	1.93	0.04
5	1.65	0.027

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				0.682
1				0.671

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.

55 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.

Ligand	Source crystal	MW · LogP · TPSA	Lipinski	PAINS	SMILES
AYC	2WOQ 1.75 Å Open crystal	187.2 Da LogP -0.06 TPSA 83.5	✓ Ro5	✓ Clean	`C[C@H](C(=O)CCC(=O)O)NC(=O)C`
LAF	1GZG 1.66 Å Open crystal	134.1 Da LogP 0.39 TPSA 54.4	✓ Ro5	✓ Clean	`C(CC(=O)O)C(=O)CF`
PE5	2WOQ 1.75 Å Open crystal	398.5 Da LogP 0.13 TPSA 94.1	✓ Ro5	✓ Clean	`CCOCCOCCOCCOCCOCCOCCOCCOCCO`
SHF	1B4K 1.67 Å Open crystal	116.1 Da LogP 0.44 TPSA 54.4	✓ Ro5	✓ Clean	`CC(=O)CCC(=O)O`

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).

Ligand	pchembl	MW · LogP · TPSA	Lipinski	PAINS	SMILES
CHEMBL2430574	—	473.5 Da LogP 4.84 TPSA 84.2	✓ Ro5	✓ Clean	`O=C(O)c1ccc2c(c1)nc(CCNC(=O)c1cccs1)n2Cc1cccc(C…`

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
ZINC5650743	1.000	222.3 Da LogP 0.07 TPSA 57.2	✓ Ro5	✓ Clean	`CCOCCOCCOCCOCCO`
ZINC6403917	1.000	354.4 Da LogP 0.11 TPSA 84.8	✓ Ro5	✓ Clean	`CCOCCOCCOCCOCCOCCOCCOCCO`
ZINC12501520	0.688	458.5 Da LogP -0.88 TPSA 123.5	1 viol.	✓ Clean	`OCCOCCOCCOCCOCCOCCOCCOCCOCCOCCO`
ZINC3874716	0.688	414.5 Da LogP -0.90 TPSA 114.3	✓ Ro5	✓ Clean	`OCCOCCOCCOCCOCCOCCOCCOCCOCCO`
ZINC4283769	0.688	238.3 Da LogP -0.96 TPSA 77.4	✓ Ro5	✓ Clean	`OCCOCCOCCOCCOCCO`
ZINC4521548	0.688	282.3 Da LogP -0.95 TPSA 86.6	✓ Ro5	✓ Clean	`OCCOCCOCCOCCOCCOCCO`
ZINC5178829	0.688	326.4 Da LogP -0.93 TPSA 95.8	✓ Ro5	✓ Clean	`OCCOCCOCCOCCOCCOCCOCCO`
ZINC5178830	0.688	370.4 Da LogP -0.91 TPSA 105.1	✓ Ro5	✓ Clean	`OCCOCCOCCOCCOCCOCCOCCOCCO`
ZINC5859031	0.688	294.4 Da LogP 1.13 TPSA 55.4	✓ Ro5	✓ Clean	`CCOCCOCCOCCOCCOCCOCC`
ZINC14619253	0.632	214.3 Da LogP 3.17 TPSA 54.4	✓ Ro5	✓ Clean	`CC(=O)CCCCCCCCCC(=O)O`
ZINC1841307	0.632	228.3 Da LogP 3.56 TPSA 54.4	✓ Ro5	✓ Clean	`CC(=O)CCCCCCCCCCC(=O)O`
ZINC1845839	0.632	200.3 Da LogP 2.78 TPSA 54.4	✓ Ro5	✓ Clean	`CC(=O)CCCCCCCCC(=O)O`
ZINC33822328	0.632	270.4 Da LogP 4.73 TPSA 54.4	✓ Ro5	✓ Clean	`CC(=O)CCCCCCCCCCCCCC(=O)O`
ZINC5855130	0.632	242.4 Da LogP 3.95 TPSA 54.4	✓ Ro5	✓ Clean	`CC(=O)CCCCCCCCCCCC(=O)O`
ZINC1644613	0.619	206.3 Da LogP 0.83 TPSA 47.9	✓ Ro5	✓ Clean	`CCCCOCCOCCOCCO`
ZINC1580161	0.600	208.3 Da LogP -0.33 TPSA 57.2	✓ Ro5	✓ Clean	`COCCOCCOCCOCCO`
ZINC16052118	0.600	340.4 Da LogP -0.28 TPSA 84.8	✓ Ro5	✓ Clean	`COCCOCCOCCOCCOCCOCCOCCO`
ZINC16052257	0.600	384.5 Da LogP -0.26 TPSA 94.1	✓ Ro5	✓ Clean	`COCCOCCOCCOCCOCCOCCOCCOCCO`
ZINC34317654	0.600	472.6 Da LogP -0.23 TPSA 112.5	1 viol.	✓ Clean	`COCCOCCOCCOCCOCCOCCOCCOCCOCCOCCO`
ZINC44076059	0.600	428.5 Da LogP -0.24 TPSA 103.3	✓ Ro5	✓ Clean	`COCCOCCOCCOCCOCCOCCOCCOCCOCCO`
ZINC5210101	0.600	252.3 Da LogP -0.31 TPSA 66.4	✓ Ro5	✓ Clean	`COCCOCCOCCOCCOCCO`
ZINC5997860	0.600	296.4 Da LogP -0.29 TPSA 75.6	✓ Ro5	✓ Clean	`COCCOCCOCCOCCOCCOCCO`
ZINC2555269	0.591	220.3 Da LogP 1.22 TPSA 47.9	✓ Ro5	✓ Clean	`CCCCCOCCOCCOCCO`
ZINC4974293	0.579	280.4 Da LogP 1.08 TPSA 55.4	✓ Ro5	✓ Clean	`CCOCCOCCOCOCCOCCOCC`
ZINC31166903	0.576	243.3 Da LogP 1.36 TPSA 83.5	✓ Ro5	✓ Clean	`CC(=O)N[C@H](C)C(=O)CCCC[C@H](C)C(=O)O`
ZINC31166908	0.576	243.3 Da LogP 1.36 TPSA 83.5	✓ Ro5	✓ Clean	`CC(=O)N[C@H](C)C(=O)CCCC[C@@H](C)C(=O)O`
ZINC31166912	0.576	243.3 Da LogP 1.36 TPSA 83.5	✓ Ro5	✓ Clean	`CC(=O)N[C@@H](C)C(=O)CCCC[C@H](C)C(=O)O`
ZINC31166917	0.576	243.3 Da LogP 1.36 TPSA 83.5	✓ Ro5	✓ Clean	`CC(=O)N[C@@H](C)C(=O)CCCC[C@@H](C)C(=O)O`
ZINC100014200	0.565	494.7 Da LogP 4.02 TPSA 84.8	✓ Ro5	✓ Clean	`CCCCCCCCCCCCOCCOCCOCCOCCOCCOCCOCCO`
ZINC100070166	0.565	290.4 Da LogP 3.17 TPSA 47.9	✓ Ro5	✓ Clean	`CCCCCCCCCCOCCOCCOCCO`
ZINC100310628	0.565	478.7 Da LogP 4.78 TPSA 75.6	✓ Ro5	✓ Clean	`CCCCCCCCCCCCCCOCCOCCOCCOCCOCCOCCO`
ZINC100365196	0.565	302.5 Da LogP 4.71 TPSA 38.7	✓ Ro5	✓ Clean	`CCCCCCCCCCCCCCOCCOCCO`
ZINC101772322	0.565	434.7 Da LogP 4.76 TPSA 66.4	✓ Ro5	✓ Clean	`CCCCCCCCCCCCCCOCCOCCOCCOCCOCCO`
ZINC103600921	0.565	466.7 Da LogP 3.24 TPSA 84.8	✓ Ro5	✓ Clean	`CCCCCCCCCCOCCOCCOCCOCCOCCOCCOCCO`
ZINC14880431	0.565	378.6 Da LogP 3.20 TPSA 66.4	✓ Ro5	✓ Clean	`CCCCCCCCCCOCCOCCOCCOCCOCCO`
ZINC14881140	0.565	306.4 Da LogP 2.41 TPSA 57.2	✓ Ro5	✓ Clean	`CCCCCCCCOCCOCCOCCOCCO`
ZINC16051619	0.565	350.5 Da LogP 2.42 TPSA 66.4	✓ Ro5	✓ Clean	`CCCCCCCCOCCOCCOCCOCCOCCO`
ZINC2584424	0.565	218.3 Da LogP 2.37 TPSA 38.7	✓ Ro5	✓ Clean	`CCCCCCCCOCCOCCO`
ZINC4521877	0.565	234.3 Da LogP 1.61 TPSA 47.9	✓ Ro5	✓ Clean	`CCCCCCOCCOCCOCCO`
ZINC58538366	0.565	392.6 Da LogP 3.59 TPSA 66.4	✓ Ro5	✓ Clean	`CCCCCCCCCCCOCCOCCOCCOCCOCCO`
ZINC58631420	0.565	422.6 Da LogP 3.22 TPSA 75.6	✓ Ro5	✓ Clean	`CCCCCCCCCCOCCOCCOCCOCCOCCOCCO`
ZINC59441819	0.565	318.5 Da LogP 3.95 TPSA 47.9	✓ Ro5	✓ Clean	`CCCCCCCCCCCCOCCOCCOCCO`
ZINC59622400	0.565	274.4 Da LogP 3.93 TPSA 38.7	✓ Ro5	✓ Clean	`CCCCCCCCCCCCOCCOCCO`
ZINC71788551	0.565	334.5 Da LogP 3.19 TPSA 57.2	✓ Ro5	✓ Clean	`CCCCCCCCCCOCCOCCOCCOCCO`
ZINC71788564	0.565	262.4 Da LogP 2.39 TPSA 47.9	✓ Ro5	✓ Clean	`CCCCCCCCOCCOCCOCCO`
ZINC71788567	0.565	406.6 Da LogP 3.98 TPSA 66.4	✓ Ro5	✓ Clean	`CCCCCCCCCCCCOCCOCCOCCOCCOCCO`
ZINC8214594	0.565	362.6 Da LogP 3.97 TPSA 57.2	✓ Ro5	✓ Clean	`CCCCCCCCCCCCOCCOCCOCCOCCO`
ZINC88260008	0.565	390.6 Da LogP 4.75 TPSA 57.2	✓ Ro5	✓ Clean	`CCCCCCCCCCCCCCOCCOCCOCCOCCO`
ZINC95784968	0.565	450.7 Da LogP 4.00 TPSA 75.6	✓ Ro5	✓ Clean	`CCCCCCCCCCCCOCCOCCOCCOCCOCCOCCO`
ZINC95863931	0.565	464.7 Da LogP 4.39 TPSA 75.6	✓ Ro5	✓ Clean	`CCCCCCCCCCCCCOCCOCCOCCOCCOCCOCCO`

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.