Protein profile

KP13_02102

Delta-aminolevulinic acid dehydratase

Genome: KpKP13

Gene: hemB AHE46102.1 Structure source: AlphaFold + ColabFold UniProt A0A0H3GNW5

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Amino acids 324

Annotations 7

Features 27

PDB binders 7

Druggability 0.454

Overview

Basic information about this protein and its source genome.

Accession: KP13_02102
Assembly: Klebsiella pneumoniae subsp. pneumoniae Kp13, complete sequence
Gene: hemB AHE46102.1
Status: annotated
Amino acids: 324
Structure source: AlphaFold + ColabFold

4.2.1.24

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. GO:0004655 Catalysis of the reaction: 2 5-aminolevulinate = 2 H2O + H+ + porphobilinogen. GO:0046872 Binding to a metal ion. GO:0005829 The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes. GO:0008270 Binding to a zinc ion (Zn). 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 (%): 42.384
Human E-value: 3.93e-76
Gut microbiome off-target: hit
Essential (DEG): Y
DEG identity (%): 92.593
DEG E-value: 0.0
Localization: Cytoplasmic
ColabFold pLDDT: 96.57

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 0.454

Structure A0A0H3GNW5

Pocket Pocket 1

P2Rank 0.587

Structure A0A0H3GNW5

Pocket Pocket 1

ColabFold model

FPocket 0.163 · Pocket 4

P2Rank 0.372 · Pocket 1

Core conservation Conserved core gene

Roary core

CoreCruncher core

Gut microbiome 413 / 4744 genomes with a hit

Normalized 0.087

Sequence

Primary amino-acid sequence viewer.

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 6 GO

Enzyme Commission (EC)

4.2.1.24

Gene Ontology (GO)

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.
GO:0004655 Catalysis of the reaction: 2 5-aminolevulinate = 2 H2O + H+ + porphobilinogen.
GO:0046872 Binding to a metal ion.
GO:0005829 The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
GO:0008270 Binding to a zinc ion (Zn).
GO:0006782 The chemical reactions and pathways resulting in the formation of protoporphyrinogen IX.

Sequence Features

Domain/signature hits from InterPro and related databases.

27 records

Show feature table

Start	End	DB	Term	Name
1	323	PIRSF	PIRSF001415	Porphbilin_synth
1	323	InterPro	IPR001731	Delta-aminolevulinic acid dehydratase
4	319	SUPERFAMILY	SSF51569	Aldolase
2	323	FunFam	G3DSA:3.20.20.70:FF:000019	Delta-aminolevulinic acid dehydratase
240	252	ProSitePatterns	PS00169	Delta-aminolevulinic acid dehydratase active site.
240	252	InterPro	IPR030656	Delta-aminolevulinic acid dehydratase, active site
265	280	PRINTS	PR00144	Delta-aminolevulinic acid dehydratase signature
265	280	InterPro	IPR001731	Delta-aminolevulinic acid dehydratase
151	170	PRINTS	PR00144	Delta-aminolevulinic acid dehydratase signature
151	170	InterPro	IPR001731	Delta-aminolevulinic acid dehydratase
295	314	PRINTS	PR00144	Delta-aminolevulinic acid dehydratase signature
295	314	InterPro	IPR001731	Delta-aminolevulinic acid dehydratase
240	256	PRINTS	PR00144	Delta-aminolevulinic acid dehydratase signature
240	256	InterPro	IPR001731	Delta-aminolevulinic acid dehydratase
189	208	PRINTS	PR00144	Delta-aminolevulinic acid dehydratase signature
189	208	InterPro	IPR001731	Delta-aminolevulinic acid dehydratase
121	135	PRINTS	PR00144	Delta-aminolevulinic acid dehydratase signature
121	135	InterPro	IPR001731	Delta-aminolevulinic acid dehydratase
6	319	Pfam	PF00490	Delta-aminolevulinic acid dehydratase
6	319	InterPro	IPR001731	Delta-aminolevulinic acid dehydratase
3	321	SMART	SM01004	ALAD_2
3	321	InterPro	IPR001731	Delta-aminolevulinic acid dehydratase
9	320	CDD	cd00384	ALAD_PBGS
2	324	Gene3D	G3DSA:3.20.20.70	Aldolase class I
2	324	InterPro	IPR013785	Aldolase-type TIM barrel
4	319	PANTHER	PTHR11458	DELTA-AMINOLEVULINIC ACID DEHYDRATASE
4	319	InterPro	IPR001731	Delta-aminolevulinic acid dehydratase

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_A0A0H3GNW5	AlphaFold	—	—	full sequence	—	Viewing
ColabFold KP13_02102	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
1				0.454
18				0.219

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	9.57	0.514
2	3.93	0.155
3	1.89	0.038
4	1.69	0.029

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	6.37	0.32
2	3.42	0.123
3	2.09	0.047

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.

58 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
4OX	1L6Y	P0ACB2	216.2 Da LogP 1.46 TPSA 91.7	✓ Ro5	✓ Clean	`C(CCC(=O)CCC(=O)O)CCC(=O)O`
AYC	2WOQ	Q59643	187.2 Da LogP -0.06 TPSA 83.5	✓ Ro5	✓ Clean	`C[C@H](C(=O)CCC(=O)O)NC(=O)C`
DSB	1I8J	P0ACB2	230.2 Da LogP 0.63 TPSA 108.7	✓ Ro5	✓ Clean	`C(CC(=O)CCC(=O)O)C(=O)CCC(=O)O`
LAF	1GZG	Q59643	134.1 Da LogP 0.39 TPSA 54.4	✓ Ro5	✓ Clean	`C(CC(=O)O)C(=O)CF`
PBG	5MHB	P0ACB2	226.2 Da LogP 0.12 TPSA 116.4	✓ Ro5	✓ Clean	`c1c(c(c([nH]1)CN)CC(=O)O)CCC(=O)O`
PE5	2WOQ	Q59643	398.5 Da LogP 0.13 TPSA 94.1	✓ Ro5	✓ Clean	`CCOCCOCCOCCOCCOCCOCCOCCOCCO`
SHF	1B4E	P0ACB2	116.1 Da LogP 0.44 TPSA 54.4	✓ Ro5	✓ Clean	`CC(=O)CCC(=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).

Ligand	UniProt (homolog)	pchembl	MW · LogP · TPSA	Lipinski	PAINS	SMILES
CHEMBL2430574	P0ACB2	—	473.5 Da LogP 4.84 TPSA 84.2	✓ Ro5	✓ Clean	`O=C(O)c1ccc2c(c1)nc(CCNC(=O)c1cccs1)n2Cc1cccc(C…`

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
ZINC35465466	1.000	244.3 Da LogP 2.24 TPSA 91.7	✓ Ro5	✓ Clean	`O=C(O)CCCCCCCC(=O)CCC(=O)O`
ZINC5650743	1.000	222.3 Da LogP 0.07 TPSA 57.2	✓ Ro5	✓ Clean	`CCOCCOCCOCCOCCO`
ZINC56609	1.000	226.2 Da LogP 0.12 TPSA 116.4	✓ Ro5	✓ Clean	`NCc1[nH]cc(CCC(=O)O)c1CC(=O)O`
ZINC6403917	1.000	354.4 Da LogP 0.11 TPSA 84.8	✓ Ro5	✓ Clean	`CCOCCOCCOCCOCCOCCOCCOCCO`
ZINC26897400	0.882	286.4 Da LogP 3.41 TPSA 91.7	✓ Ro5	✓ Clean	`O=C(O)CCCCCCC(=O)CCCCCCC(=O)O`
ZINC3074813	0.882	258.3 Da LogP 2.63 TPSA 91.7	✓ Ro5	✓ Clean	`O=C(O)CCCCCC(=O)CCCCCC(=O)O`
ZINC34423725	0.882	342.5 Da LogP 4.97 TPSA 91.7	✓ Ro5	✓ Clean	`O=C(O)CCCCCCCCC(=O)CCCCCCCCC(=O)O`
ZINC4822898	0.882	272.3 Da LogP 3.02 TPSA 91.7	✓ Ro5	✓ Clean	`O=C(O)CCCCCCC(=O)CCCCCC(=O)O`
ZINC4822900	0.882	300.4 Da LogP 3.80 TPSA 91.7	✓ Ro5	✓ Clean	`O=C(O)CCCCCCCCC(=O)CCCCCC(=O)O`
ZINC3074815	0.833	230.3 Da LogP 1.85 TPSA 91.7	✓ Ro5	✓ Clean	`O=C(O)CCCCCC(=O)CCCC(=O)O`
ZINC2508031	0.824	230.3 Da LogP 1.85 TPSA 91.7	✓ Ro5	✓ Clean	`O=C(O)CCCCC(=O)CCCCC(=O)O`
ZINC4727003	0.727	312.4 Da LogP 4.69 TPSA 71.4	✓ Ro5	✓ Clean	`CCCCCCC(=O)CCC(=O)CCCCCCCC(=O)O`
ZINC59545317	0.727	200.3 Da LogP 2.78 TPSA 54.4	✓ Ro5	✓ Clean	`CCCCCCCC(=O)CCC(=O)O`
ZINC59545320	0.727	270.4 Da LogP 4.73 TPSA 54.4	✓ Ro5	✓ Clean	`CCCCCCCCCCCCC(=O)CCC(=O)O`
ZINC59545336	0.727	214.3 Da LogP 3.17 TPSA 54.4	✓ Ro5	✓ Clean	`CCCCCCCCC(=O)CCC(=O)O`
ZINC1703342	0.722	202.2 Da LogP 1.07 TPSA 91.7	✓ Ro5	✓ Clean	`O=C(O)CCCC(=O)CCCC(=O)O`
ZINC113465827	0.714	286.4 Da LogP 3.70 TPSA 74.6	✓ Ro5	✓ Clean	`O=C(O)CCCCC(=O)CCCCCCCCCCO`
ZINC1529497	0.706	230.3 Da LogP 3.06 TPSA 74.6	✓ Ro5	✓ Clean	`O=C(O)CCCCCCCCCCC(=O)O`
ZINC1531045	0.706	202.2 Da LogP 2.28 TPSA 74.6	✓ Ro5	✓ Clean	`O=C(O)CCCCCCCCC(=O)O`
ZINC1593115	0.706	216.3 Da LogP 2.67 TPSA 74.6	✓ Ro5	✓ Clean	`O=C(O)CCCCCCCCCC(=O)O`
ZINC1700020	0.706	244.3 Da LogP 3.45 TPSA 74.6	✓ Ro5	✓ Clean	`O=C(O)CCCCCCCCCCCC(=O)O`
ZINC3860440	0.706	258.4 Da LogP 3.84 TPSA 74.6	✓ Ro5	✓ Clean	`O=C(O)CCCCCCCCCCCCC(=O)O`
ZINC3861298	0.706	286.4 Da LogP 4.62 TPSA 74.6	✓ Ro5	✓ Clean	`O=C(O)CCCCCCCCCCCCCCC(=O)O`
ZINC5113062	0.706	272.4 Da LogP 4.23 TPSA 74.6	✓ Ro5	✓ Clean	`O=C(O)CCCCCCCCCCCCCC(=O)O`
ZINC33822324	0.696	228.3 Da LogP 2.35 TPSA 71.4	✓ Ro5	✓ Clean	`O=CCCC(=O)CCCCCCCC(=O)O`
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`
ZINC138457918	0.682	228.3 Da LogP 3.56 TPSA 54.4	✓ Ro5	✓ Clean	`CCCCCCCC(=O)CCCCC(=O)O`
ZINC138458029	0.682	228.3 Da LogP 3.56 TPSA 54.4	✓ Ro5	✓ Clean	`CCCCCCC(=O)CCCCCC(=O)O`
ZINC144395054	0.682	242.4 Da LogP 3.95 TPSA 54.4	✓ Ro5	✓ Clean	`CCCCCC(=O)CCCCCCCC(=O)O`
ZINC196749828	0.682	214.3 Da LogP 3.17 TPSA 54.4	✓ Ro5	✓ Clean	`CCCCCCC(=O)CCCCC(=O)O`
ZINC2113934076	0.682	256.4 Da LogP 4.34 TPSA 54.4	✓ Ro5	✓ Clean	`CCCCCCC(=O)CCCCCCCC(=O)O`
ZINC2113934081	0.682	270.4 Da LogP 4.73 TPSA 54.4	✓ Ro5	✓ Clean	`CCCCC(=O)CCCCCCCCCCC(=O)O`
ZINC2113934082	0.682	256.4 Da LogP 4.34 TPSA 54.4	✓ Ro5	✓ Clean	`CCCCCCCC(=O)CCCCCCC(=O)O`
ZINC2113934083	0.682	256.4 Da LogP 4.34 TPSA 54.4	✓ Ro5	✓ Clean	`CCCCCCCCCC(=O)CCCCC(=O)O`
ZINC2243668	0.682	214.3 Da LogP 3.17 TPSA 54.4	✓ Ro5	✓ Clean	`CCCCC(=O)CCCCCCC(=O)O`
ZINC2243670	0.682	228.3 Da LogP 3.56 TPSA 54.4	✓ Ro5	✓ Clean	`CCCCCC(=O)CCCCCCC(=O)O`
ZINC2378799	0.682	200.3 Da LogP 2.78 TPSA 54.4	✓ Ro5	✓ Clean	`CCCCC(=O)CCCCCC(=O)O`
ZINC2378809	0.682	200.3 Da LogP 2.78 TPSA 54.4	✓ Ro5	✓ Clean	`CCCC(=O)CCCCCCC(=O)O`
ZINC3074822	0.682	229.3 Da LogP 2.11 TPSA 80.4	✓ Ro5	✓ Clean	`NCCCCCC(=O)CCCCCC(=O)O`
ZINC33820423	0.682	242.4 Da LogP 3.95 TPSA 54.4	✓ Ro5	✓ Clean	`CCCCC(=O)CCCCCCCCC(=O)O`
ZINC4822737	0.682	313.5 Da LogP 4.45 TPSA 80.4	✓ Ro5	✓ Clean	`NCCCCCCCCCCCC(=O)CCCCCC(=O)O`
ZINC5973005	0.682	242.4 Da LogP 3.95 TPSA 54.4	✓ Ro5	✓ Clean	`CCCCCCC(=O)CCCCCCC(=O)O`
ZINC79244776	0.682	270.4 Da LogP 4.73 TPSA 54.4	✓ Ro5	✓ Clean	`CCCCCCCC(=O)CCCCCCCC(=O)O`
ZINC86039283	0.682	242.4 Da LogP 3.95 TPSA 54.4	✓ Ro5	✓ Clean	`CCCCCCCCC(=O)CCCCC(=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.