Protein profile

KP13_00801

Uracil-DNA glycosylase

Genome: KpKP13

Gene: ung AHE43166.1 Structure source: AlphaFold + ColabFold UniProt A0A0H3GTU7

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Amino acids 237

Annotations 7

Features 20

PDB binders 16

Druggability 0.357

Overview

Basic information about this protein and its source genome.

Accession: KP13_00801
Assembly: Klebsiella pneumoniae subsp. pneumoniae Kp13, complete sequence
Gene: ung AHE43166.1
Status: annotated
Amino acids: 237
Structure source: AlphaFold + ColabFold

3.2.2.27

GO:0006284 In base excision repair, an altered base is removed by a DNA glycosylase enzyme, followed by excision of the resulting sugar phosphate. The small gap left in the DNA helix is filled in by the sequential action of DNA polymerase and DNA ligase. GO:0004844 Catalysis of the cleavage of the N-C1' glycosidic bond between the damaged DNA base and the deoxyribose sugar, releasing a free base and leaving an apyrimidinic (AP) site. Enzymes with this activity recognize and remove uracil bases in DNA that result from the deamination of cytosine or the misincorporation of dUTP opposite an adenine. GO:0016799 Catalysis of the hydrolysis of any N-glycosyl bond. GO:0006281 The process of restoring DNA after damage. Genomes are subject to damage by chemical and physical agents in the environment (e.g. UV and ionizing radiations, chemical mutagens, fungal and bacterial toxins, etc.) and by free radicals or alkylating agents endogenously generated in metabolism. DNA is also damaged because of errors during its replication. A variety of different DNA repair pathways have been reported that include direct reversal, base excision repair, nucleotide excision repair, photoreactivation, bypass, double-strand break repair pathway, and mismatch repair pathway. GO:0005737 The contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures. GO:0097510 A base-excision repair, AP site formation process occurring via excision of a deaminated base.

Target profile

Computed evidence for target prioritization.

Human off-target: hit
Human identity (%): 64.848
Human E-value: 1.46e-72
Gut microbiome off-target: hit
Essential (DEG): Y
DEG identity (%): 71.628
DEG E-value: 3.34e-113
Localization: Cytoplasmic
ColabFold pLDDT: 95.24

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 0.357

Structure A0A0H3GTU7

Pocket Pocket 5

P2Rank 0.429

Structure A0A0H3GTU7

Pocket Pocket 1

ColabFold model

FPocket 0.214 · Pocket 10

P2Rank 0.341 · Pocket 1

Core conservation Conserved core gene

Roary core

CoreCruncher core

Gut microbiome 2006 / 4744 genomes with a hit

Normalized 0.423

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)

3.2.2.27

Gene Ontology (GO)

GO:0006284 In base excision repair, an altered base is removed by a DNA glycosylase enzyme, followed by excision of the resulting sugar phosphate. The small gap left in the DNA helix is filled in by the sequential action of DNA polymerase and DNA ligase.
GO:0004844 Catalysis of the cleavage of the N-C1' glycosidic bond between the damaged DNA base and the deoxyribose sugar, releasing a free base and leaving an apyrimidinic (AP) site. Enzymes with this activity recognize and remove uracil bases in DNA that result from the deamination of cytosine or the misincorporation of dUTP opposite an adenine.
GO:0016799 Catalysis of the hydrolysis of any N-glycosyl bond.
GO:0006281 The process of restoring DNA after damage. Genomes are subject to damage by chemical and physical agents in the environment (e.g. UV and ionizing radiations, chemical mutagens, fungal and bacterial toxins, etc.) and by free radicals or alkylating agents endogenously generated in metabolism. DNA is also damaged because of errors during its replication. A variety of different DNA repair pathways have been reported that include direct reversal, base excision repair, nucleotide excision repair, photoreactivation, bypass, double-strand break repair pathway, and mismatch repair pathway.
GO:0005737 The contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
GO:0097510 A base-excision repair, AP site formation process occurring via excision of a deaminated base.

Sequence Features

Domain/signature hits from InterPro and related databases.

20 records

Show feature table

Start	End	DB	Term	Name
11	237	Gene3D	G3DSA:3.40.470.10	-
11	237	InterPro	IPR036895	Uracil-DNA glycosylase-like domain superfamily
57	218	SMART	SM00987	UDG_2_a
27	228	CDD	cd10027	UDG-F1-like
27	228	InterPro	IPR002043	Uracil-DNA glycosylase family 1
57	218	SMART	SM00986	UDG_2
57	218	InterPro	IPR005122	Uracil-DNA glycosylase-like
12	228	SUPERFAMILY	SSF52141	Uracil-DNA glycosylase-like
12	228	InterPro	IPR036895	Uracil-DNA glycosylase-like domain superfamily
5	232	FunFam	G3DSA:3.40.470.10:FF:000001	Uracil-DNA glycosylase
14	221	NCBIfam	TIGR00628	uracil-DNA glycosylase
14	221	InterPro	IPR002043	Uracil-DNA glycosylase family 1
12	229	Hamap	MF_00148	Uracil-DNA glycosylase [ung].
12	229	InterPro	IPR002043	Uracil-DNA glycosylase family 1
4	230	PANTHER	PTHR11264	URACIL-DNA GLYCOSYLASE
4	230	InterPro	IPR002043	Uracil-DNA glycosylase family 1
65	74	ProSitePatterns	PS00130	Uracil-DNA glycosylase signature.
65	74	InterPro	IPR018085	Uracil-DNA glycosylase, active site
63	217	Pfam	PF03167	Uracil DNA glycosylase superfamily
63	217	InterPro	IPR005122	Uracil-DNA glycosylase-like

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_A0A0H3GTU7	AlphaFold	—	—	full sequence	—	Viewing
ColabFold KP13_00801	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
5				0.357
3				0.252

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	Sticks	Spheres	Surfaces	Score	Probability	Labels	Zoom	Positions
1				5.45	0.259

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
10				0.214

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	Sticks	Spheres	Surfaces	Score	Probability	Labels	Zoom	Positions
1				4.52	0.193
2				1.87	0.037

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.

67 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
302	2HXM	P13051	346.3 Da LogP 0.16 TPSA 146.2	✓ Ro5	✓ Clean	`c1cc(ccc1\C=N\OCCO/N=C/C2=CC(=O)NC(=O)N2)C(=O)O`
3FI	3FCI	P13051	346.3 Da LogP 0.29 TPSA 136.6	✓ Ro5	✓ Clean	`c1cc(cc(c1)C(=O)O)\C=N\OCCCNCC2=CC(=O)NC(=O)N2`
3FL	3FCL	P13051	346.4 Da LogP 0.42 TPSA 127.1	✓ Ro5	✓ Clean	`c1cc(cc(c1)C(=O)O)CNCCCCNCC2=CC(=O)NC(=O)N2`
5NU	4WS4	P9WFQ9	157.1 Da LogP -1.03 TPSA 108.9	✓ Ro5	✓ Clean	`C1=C(C(=O)NC(=O)N1)[N+](=O)[O-]`
5UC	4WS7	P9WFQ9	146.5 Da LogP -0.28 TPSA 65.7	✓ Ro5	✓ Clean	`C1=C(C(=O)NC(=O)N1)Cl`
6UA	4WS2	P9WFQ9	127.1 Da LogP -1.02 TPSA 84.5	✓ Ro5	✓ Clean	`C1C(=NC(=O)NC1=O)N`
DUR	2C53	P10186	228.2 Da LogP -1.82 TPSA 104.6	✓ Ro5	✓ Clean	`C1[C@@H]([C@H](O[C@H]1N2C=CC(=O)NC2=O)CO)O`
FCF	3FCF	P13051	346.3 Da LogP 0.16 TPSA 146.2	✓ Ro5	✓ Clean	`c1cc(cc(c1)C(=O)O)\C=N\OCCO/N=C/C2=CC(=O)NC(=O)…`
FCK	3FCK	P13051	346.3 Da LogP 0.29 TPSA 136.6	✓ Ro5	✓ Clean	`c1cc(cc(c1)C(=O)O)CNCCCON=CC2=CC(=O)NC(=O)N2`
FLC	3A7N	P9WFQ9	189.1 Da LogP -5.25 TPSA 140.6	✓ Ro5	✓ Clean	`C(C(=O)[O-])C(CC(=O)[O-])(C(=O)[O-])O`
QU4	6VBA	P13051	422.3 Da LogP 2.45 TPSA 169.4	✓ Ro5	✓ Clean	`c1cc(c(cc1C(=C2C=CC(=O)C(=C2)C(=O)O)c3ccc(c(c3)…`
TUL	4WS8	P9WFQ9	128.2 Da LogP 0.43 TPSA 48.6	✓ Ro5	✓ Clean	`C1=CNC(=S)NC1=O`
URA	1FLZ	P12295	112.1 Da LogP -0.94 TPSA 65.7	✓ Ro5	✓ Clean	`C1=CNC(=O)NC1=O`
URB	3CXM	D0VWU0	191.0 Da LogP -0.17 TPSA 65.7	✓ Ro5	✓ Clean	`C1=C(C(=O)NC(=O)N1)Br`
URF	4WRY	P9WFQ9	130.1 Da LogP -0.80 TPSA 65.7	✓ Ro5	✓ Clean	`C1=C(C(=O)NC(=O)N1)F`
WBU	4WS6	P9WFQ9	127.1 Da LogP -1.35 TPSA 91.7	✓ Ro5	✓ Clean	`C1=C(C(=O)NC(=O)N1)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).

Ligand	UniProt (homolog)	pchembl	MW · LogP · TPSA	Lipinski	PAINS	SMILES
CHEMBL4129274	P13051	—	851.5 Da LogP 4.76 TPSA 183.3	3 viol.	Alert	`C=CC(=O)Nc1ccccc1Nc1nc(Nc2ccc(N3CCN(CCOCCOCCOCC…`

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
ZINC105325	1.000	228.2 Da LogP -1.82 TPSA 104.6	✓ Ro5	✓ Clean	`O=c1ccn([C@@H]2C[C@@H](O)[C@H](CO)O2)c(=O)[nH]1`
ZINC155696	1.000	228.2 Da LogP -1.82 TPSA 104.6	✓ Ro5	✓ Clean	`O=c1ccn([C@H]2C[C@H](O)[C@@H](CO)O2)c(=O)[nH]1`
ZINC2556389	1.000	228.2 Da LogP -1.82 TPSA 104.6	✓ Ro5	✓ Clean	`O=c1ccn([C@H]2C[C@@H](O)[C@H](CO)O2)c(=O)[nH]1`
ZINC3635934	1.000	228.2 Da LogP -1.82 TPSA 104.6	✓ Ro5	✓ Clean	`O=c1ccn([C@@H]2C[C@H](O)[C@@H](CO)O2)c(=O)[nH]1`
ZINC3833863	1.000	422.3 Da LogP 2.45 TPSA 169.4	✓ Ro5	✓ Clean	`O=C(O)C1=CC(=C(c2ccc(O)c(C(=O)O)c2)c2ccc(O)c(C(…`
ZINC3869842	1.000	228.2 Da LogP -1.82 TPSA 104.6	✓ Ro5	✓ Clean	`O=c1ccn([C@H]2C[C@H](O)[C@H](CO)O2)c(=O)[nH]1`
ZINC4124398	1.000	228.2 Da LogP -1.82 TPSA 104.6	✓ Ro5	✓ Clean	`O=c1ccn([C@H]2C[C@@H](O)[C@@H](CO)O2)c(=O)[nH]1`
ZINC56350	1.000	228.2 Da LogP -1.82 TPSA 104.6	✓ Ro5	✓ Clean	`O=c1ccn([C@@H]2C[C@H](O)[C@H](CO)O2)c(=O)[nH]1`
ZINC8613701	1.000	228.2 Da LogP -1.82 TPSA 104.6	✓ Ro5	✓ Clean	`O=c1ccn([C@@H]2C[C@@H](O)[C@@H](CO)O2)c(=O)[nH]1`
ZINC4918789	0.850	258.2 Da LogP -2.46 TPSA 124.8	✓ Ro5	✓ Clean	`O=c1ccn([C@@H]2C[C@H](O)[C@H](O)[C@H](CO)O2)c(=…`
ZINC4918794	0.850	258.2 Da LogP -2.46 TPSA 124.8	✓ Ro5	✓ Clean	`O=c1ccn([C@H]2C[C@H](O)[C@H](O)[C@H](CO)O2)c(=O…`
ZINC4918798	0.850	258.2 Da LogP -2.46 TPSA 124.8	✓ Ro5	✓ Clean	`O=c1ccn([C@@H]2C[C@@H](O)[C@H](O)[C@H](CO)O2)c(…`
ZINC4918802	0.850	258.2 Da LogP -2.46 TPSA 124.8	✓ Ro5	✓ Clean	`O=c1ccn([C@H]2C[C@@H](O)[C@H](O)[C@H](CO)O2)c(=…`
ZINC103421486	0.762	244.3 Da LogP -0.45 TPSA 87.5	✓ Ro5	✓ Clean	`O=c1[nH]c(=S)ccn1[C@H]1C[C@@H](O)[C@@H](CO)O1`
ZINC1081178	0.762	230.2 Da LogP -0.85 TPSA 84.3	✓ Ro5	✓ Clean	`O=c1ccn([C@@H]2C[C@H](F)[C@@H](CO)O2)c(=O)[nH]1`
ZINC17173289	0.762	244.3 Da LogP -0.45 TPSA 87.5	✓ Ro5	✓ Clean	`O=c1[nH]c(=S)ccn1[C@H]1C[C@H](O)[C@@H](CO)O1`
ZINC2556998	0.762	230.2 Da LogP -0.85 TPSA 84.3	✓ Ro5	✓ Clean	`O=c1ccn([C@@H]2C[C@@H](F)[C@H](CO)O2)c(=O)[nH]1`
ZINC29544850	0.762	230.2 Da LogP -0.85 TPSA 84.3	✓ Ro5	✓ Clean	`O=c1ccn([C@@H]2C[C@@H](F)[C@@H](CO)O2)c(=O)[nH]1`
ZINC33505015	0.762	244.3 Da LogP -0.45 TPSA 87.5	✓ Ro5	✓ Clean	`O=c1ccn([C@H]2C[C@H](O)[C@@H](CO)O2)c(=S)[nH]1`
ZINC3792179	0.762	230.2 Da LogP -0.85 TPSA 84.3	✓ Ro5	✓ Clean	`O=c1ccn([C@H]2C[C@H](F)[C@@H](CO)O2)c(=O)[nH]1`
ZINC4975368	0.762	230.2 Da LogP -0.85 TPSA 84.3	✓ Ro5	✓ Clean	`O=c1ccn([C@@H]2C[C@H](F)[C@H](CO)O2)c(=O)[nH]1`
ZINC2054344316	0.756	300.3 Da LogP 2.01 TPSA 111.9	✓ Ro5	✓ Clean	`CC(=C1C=CC(=O)C(C(=O)O)=C1)c1ccc(O)c(C(=O)O)c1`
ZINC28092924	0.756	300.3 Da LogP 2.01 TPSA 111.9	✓ Ro5	✓ Clean	`C/C(=C1/C=CC(=O)C(C(=O)O)=C1)c1ccc(O)c(C(=O)O)c1`
ZINC36748824	0.756	300.3 Da LogP 2.01 TPSA 111.9	✓ Ro5	✓ Clean	`C/C(=C1\C=CC(=O)C(C(=O)O)=C1)c1ccc(O)c(C(=O)O)c1`
ZINC1532902	0.700	206.2 Da LogP -0.86 TPSA 132.1	✓ Ro5	✓ Clean	`O=C(O)CC[C@@](O)(CC(=O)O)C(=O)O`
ZINC2018106	0.700	206.2 Da LogP -0.86 TPSA 132.1	✓ Ro5	✓ Clean	`O=C(O)CC[C@](O)(CC(=O)O)C(=O)O`
ZINC13514392	0.696	308.2 Da LogP -1.71 TPSA 151.1	✓ Ro5	✓ Clean	`O=c1ccn([C@@H]2C[C@@H](O)[C@@H](COP(=O)(O)O)O2)…`
ZINC1532629	0.696	308.2 Da LogP -1.71 TPSA 151.1	✓ Ro5	✓ Clean	`O=c1ccn([C@@H]2C[C@@H](O)[C@H](COP(=O)(O)O)O2)c…`
ZINC3869888	0.696	308.2 Da LogP -1.71 TPSA 151.1	✓ Ro5	✓ Clean	`O=c1ccn([C@@H]2C[C@H](O)[C@H](COP(=O)(O)O)O2)c(…`
ZINC3869889	0.696	308.2 Da LogP -1.71 TPSA 151.1	✓ Ro5	✓ Clean	`O=c1ccn([C@H]2C[C@H](O)[C@H](COP(=O)(O)O)O2)c(=…`
ZINC3869890	0.696	308.2 Da LogP -1.71 TPSA 151.1	✓ Ro5	✓ Clean	`O=c1ccn([C@H]2C[C@@H](O)[C@H](COP(=O)(O)O)O2)c(…`
ZINC4228260	0.696	308.2 Da LogP -1.71 TPSA 151.1	✓ Ro5	✓ Clean	`O=c1ccn([C@H]2C[C@H](O)[C@@H](COP(=O)(O)O)O2)c(…`
ZINC6524723	0.696	308.2 Da LogP -1.71 TPSA 151.1	✓ Ro5	✓ Clean	`O=c1ccn([C@@H]2C[C@H](O)[C@@H](COP(=O)(O)O)O2)c…`
ZINC3787626	0.681	253.2 Da LogP -0.50 TPSA 133.1	✓ Ro5	Alert	`[N-]=[N+]=N[C@H]1C[C@H](n2ccc(=O)[nH]c2=O)O[C@@…`
ZINC5663432	0.681	253.2 Da LogP -0.50 TPSA 133.1	✓ Ro5	Alert	`[N-]=[N+]=N[C@H]1C[C@@H](n2ccc(=O)[nH]c2=O)O[C@…`
ZINC5663433	0.681	253.2 Da LogP -0.50 TPSA 133.1	✓ Ro5	Alert	`[N-]=[N+]=N[C@H]1C[C@H](n2ccc(=O)[nH]c2=O)O[C@H…`
ZINC5663434	0.681	253.2 Da LogP -0.50 TPSA 133.1	✓ Ro5	Alert	`[N-]=[N+]=N[C@@H]1C[C@@H](n2ccc(=O)[nH]c2=O)O[C…`
ZINC5663435	0.681	253.2 Da LogP -0.50 TPSA 133.1	✓ Ro5	Alert	`[N-]=[N+]=N[C@@H]1C[C@H](n2ccc(=O)[nH]c2=O)O[C@…`
ZINC6524816	0.681	253.2 Da LogP -0.50 TPSA 133.1	✓ Ro5	Alert	`[N-]=[N+]=N[C@@H]1C[C@H](n2ccc(=O)[nH]c2=O)O[C@…`
ZINC38322194	0.667	254.2 Da LogP -1.26 TPSA 134.6	✓ Ro5	Alert	`N=[N+]=N[C@@H]1C[C@@H](n2ccc(=O)[nH]c2=O)O[C@H]…`
ZINC38322195	0.667	254.2 Da LogP -1.26 TPSA 134.6	✓ Ro5	Alert	`N=[N+]=N[C@@H]1C[C@H](n2ccc(=O)[nH]c2=O)O[C@H]1…`
ZINC3870698	0.667	212.2 Da LogP -0.80 TPSA 84.3	✓ Ro5	✓ Clean	`C[C@H]1O[C@@H](n2ccc(=O)[nH]c2=O)C[C@@H]1O`
ZINC3593496	0.652	206.2 Da LogP -1.16 TPSA 121.1	✓ Ro5	✓ Clean	`COC(=O)C[C@@](O)(CC(=O)O)C(=O)O`
ZINC3593497	0.652	206.2 Da LogP -1.16 TPSA 121.1	✓ Ro5	✓ Clean	`COC(=O)C[C@](O)(CC(=O)O)C(=O)O`
ZINC13519035	0.651	229.2 Da LogP -2.43 TPSA 117.4	✓ Ro5	✓ Clean	`O=c1ncn([C@H]2C[C@H](O)[C@@H](CO)O2)c(=O)[nH]1`
ZINC64708385	0.644	467.4 Da LogP 0.44 TPSA 214.5	1 viol.	✓ Clean	`NOC(=O)C1=CC(=C(c2ccc(O)c(C(=O)ON)c2)c2ccc(O)c(…`
ZINC8217150	0.640	388.2 Da LogP -1.59 TPSA 197.6	✓ Ro5	✓ Clean	`O=c1ccn([C@H]2C[C@H](O)[C@@H](CO[P@@](=O)(O)OP(…`
ZINC2522522	0.636	244.2 Da LogP -2.12 TPSA 124.8	✓ Ro5	✓ Clean	`O=c1[nH]c(=O)n([C@@H]2C[C@@H](O)[C@H](CO)O2)cc1O`
ZINC405339	0.636	244.2 Da LogP -2.12 TPSA 124.8	✓ Ro5	✓ Clean	`O=c1[nH]c(=O)n([C@H]2C[C@H](O)[C@H](CO)O2)cc1O`
ZINC4897037	0.636	244.2 Da LogP -2.12 TPSA 124.8	✓ Ro5	✓ Clean	`O=c1[nH]c(=O)n([C@@H]2C[C@H](O)[C@H](CO)O2)cc1O`

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.