ABL1_KD · BoltzMaker

ABL1_KD packed 2026-08-23

1 Proteins

0 Co-folded partners

2 Ligands

1 Pockets

1 Apo structure references

5 Predictions

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Campaign summary

Field	Value	Details
Input file	boltz_input.md	boltz_input.md
Proteins	1	2 protein block(s) in 1 group(s): ABL1 (272 aa); ABLAP (272 aa)
Co-folded partners	0	none
Ligands	2	IMATI (SMILES); DASAT (SMILES)
Pockets	1	1N1
Apo structure references	1	ABLAP
Predictions	5	ABL1_IMATI, ABL1_IMATI_1N1, ABL1_DASAT, ABL1_DASAT_1N1, ABLAP
Predict affinity	yes	pIC50 predicted for every ligand-bound prediction
Ligand chemistry	2 of 2 flagged	IMATI, DASAT -- see "Ligand preparation" below
Boltz predict runtime	18m 11s	across 2 run invocations
Accelerator	gpu	gpu = Metal/CUDA backend used; cpu = no GPU available
Workers	0	parallel data-loading workers (Boltz's own default is 2)
MPS watermark	1.0	PYTORCH_MPS_HIGH_WATERMARK_RATIO cap -- lower avoids swap on Apple unified memory
Max parallel samples	1	Boltz's own --max_parallel_samples
Max MSA sequences	4096	cap on MSA sequences used for co-evolution features

Reference structures

The experimental structures this campaign was built on: where each pocket came from, and what the secondary-structure comparison measures against.

Pocket definitions

Pocket	From	Proteins	Contacts
1N1	2GQG	ABL1	18
STI	1IEP	ABL1	reference only

Secondary-structure references

Protein	Structure	State	Contents	Chain
ABL1	2gqg.cif	DFG-in, αC-in	2 chain(s), bound: 1N1, PTR	A

A kinase's state is its DFG motif and αC helix, taken from the secondary-structure comparison.

Ligand definitions

Ligand	Class	Given as	Experimental structure
IMATI	Control	SMILES	STI
DASAT	Control	SMILES	1N1

A control has been verified experimentally, by structure or by assay, so its prediction can be checked; an experimental compound is under investigation, with nothing to check against. Experimental compounds are ringed in red in the charts.

pIC50 vs confidence score

Click a point to open that target, in the panel below the Targets table.

pIC50 vs binder probability

Click a point to open that target, in the panel below the Targets table.

Ranked predicted pIC50

Click a point to open that target, in the panel below the Targets table.

Ranked confidence

Click a point to open that target, in the panel below the Targets table.

Summary table

Identity						Affinity		▸ Confidence (5)	▸ Interactions (5)	Structure
Run	Protein	Ligand	Pocket	Class	Summary	Binder	pIC50	Score	pTM	ipTM	Lig	pLDDT	Total	Phob	H	Salt	π	CIF
4	ABL1	DASAT	1N1	Control		0.99	12.86	0.95	0.97	0.98	0.98	0.94	10.00	7	3	0	0	CIF
2	ABL1	IMATI	1N1	Control		0.81	10.10	0.95	0.96	0.98	0.98	0.94	16.00	10	4	1	1	CIF
3	ABL1	DASAT	Unc	Control		0.55	9.89	0.88	0.69	0.88	0.88	0.88	11.00	8	3	0	0	CIF
1	ABL1	IMATI	Unc	Control		0.49	9.36	0.91	0.78	0.92	0.92	0.91	17.00	10	5	2	0	CIF
5	ABLAP	Apo	N/A	N/A	N/A	N/A	N/A	0.93	0.94	N/A	N/A	0.92	N/A	N/A	N/A	N/A	N/A	CIF

Download full CSV · Download summary CSV

🎯 affinity Likely binder (p ≥ 0.7) Uncertain (0.3-0.7) Likely non-binder (p < 0.3)

🛡️ confidence High confidence (≥ 0.7) Moderate confidence (0.5-0.7) Low confidence (< 0.5)

Predictions

One row per prediction. Click one to see its pose and interactions, in the panel below.

Flagged only

Run	Prediction	Protein	Ligand	Pocket	Class	Confidence	pIC50	Interactions	Flags

Target

Overall structure

Interaction diagram

Detected interactions

Metrics

Ligand pose

Superposed targets

Sequence

Pockets

1 named pocket(s) (1N1) plus an unconstrained baseline; contacts are enforced within 4 A.

Pocket	Protein	Ligands	Runs	Targets	Contacts
1N1	ABL1	IMATI, DASAT	2, 4	2	18 residue(s)
Unconstrained	ABL1	IMATI, DASAT	1, 3	2	none -- ligand placed freely

Where the ligands landed

Ligand preparation

2 of 2 ligand(s) flagged for chemistry review -- these are advisory, not errors; verify the input SMILES reflects what you intended before trusting the results below.

Ligand	Chemistry notes
IMATI	ionizable group(s) present (primary/secondary amine) -- verify the SMILES reflects your intended protonation state
DASAT	ionizable group(s) present (primary/secondary amine) -- verify the SMILES reflects your intended protonation state

Ligand structures

No shared scaffold or substructure detected across the set -- ligands are structurally distinct.

Sundefined stereocentreAcarboxylic acidNprimary/secondary aminePhphenolSO3sulfonic acidsaltsalt/disconnected fragment

IMATIN

MW 494 · cLogP 4.6 · TPSA 86

DASATN

MW 488 · cLogP 3.3 · TPSA 107

Download PDF · Download SMILES

Scaffolds: Bemis-Murcko, exact match first, then Tanimoto-clustered (Morgan r=2, 2048-bit, threshold 0.60) whole-group MCS as a verified fallback. Minimum highlighted substructure size: 8 heavy atoms. Stereocentre/ionizable-group highlighting from this campaign's own ligand-preparation check (see above).

Interaction counts by type

Click a point to open that target, in the panel below the Targets table.

SSE motif shifts (apo vs holo)

Identity						Shift			Boundary		Backbone	Kinase state
Family	Target	Ligand	Motif	Kind	Source	N res	RMSD (A)	Centroid delta (A)	Start delta	End delta	Flagged phi/psi	DFG apo	DFG holo	DFG delta	alphaC apo	alphaC holo	alphaC delta
ABL1	ABL1_DASAT	DASAT	DFG	loop	kinase	3	4.47	3.40	N/A	N/A	2	in	out	True	in	in	False
ABL1	ABL1_DASAT	DASAT	DFG	loop	kinase	3	0.76	0.67	N/A	N/A	0	in	in	False	in	in	False
ABL1	ABL1_DASAT	DASAT	catalytic_loop	loop	kinase	3	0.73	0.70	N/A	N/A	0	in	out	True	in	in	False
ABL1	ABL1_DASAT	DASAT	catalytic_loop	loop	kinase	3	0.43	0.41	N/A	N/A	0	in	in	False	in	in	False
ABL1	ABL1_DASAT	DASAT	hinge	loop	kinase	3	0.25	0.12	N/A	N/A	0	in	out	True	in	in	False
ABL1	ABL1_DASAT	DASAT	hinge	loop	kinase	3	0.19	0.11	N/A	N/A	0	in	in	False	in	in	False
ABL1	ABL1_DASAT	DASAT	pocket_scaffold	loop	kinase	73	1.70	0.00	-146.00	-133.00	8	in	out	True	in	in	False
ABL1	ABL1_DASAT	DASAT	pocket_scaffold	loop	kinase	73	1.25	0.00	-146.00	-133.00	8	in	in	False	in	in	False
ABL1	ABL1_DASAT	DASAT	alphaC_Glu	point	kinase	1	0.97	0.97	N/A	N/A	0	in	out	True	in	in	False
ABL1	ABL1_DASAT	DASAT	alphaC_Glu	point	kinase	1	0.90	0.90	N/A	N/A	0	in	in	False	in	in	False
ABL1	ABL1_DASAT	DASAT	catalytic_Lys	point	kinase	1	1.08	1.08	N/A	N/A	0	in	out	True	in	in	False
ABL1	ABL1_DASAT	DASAT	catalytic_Lys	point	kinase	1	0.88	0.88	N/A	N/A	0	in	in	False	in	in	False
ABL1	ABL1_DASAT	DASAT	gatekeeper	point	kinase	1	0.09	0.09	N/A	N/A	0	in	out	True	in	in	False
ABL1	ABL1_DASAT	DASAT	gatekeeper	point	kinase	1	0.15	0.15	N/A	N/A	0	in	in	False	in	in	False
ABL1	ABL1_IMATI	IMATI	DFG	loop	kinase	3	5.58	4.67	N/A	N/A	2	in	other	True	in	in	False
ABL1	ABL1_IMATI	IMATI	DFG	loop	kinase	3	5.23	4.26	N/A	N/A	2	in	other	True	in	in	False
ABL1	ABL1_IMATI	IMATI	catalytic_loop	loop	kinase	3	0.53	0.49	N/A	N/A	0	in	other	True	in	in	False
ABL1	ABL1_IMATI	IMATI	catalytic_loop	loop	kinase	3	0.65	0.62	N/A	N/A	0	in	other	True	in	in	False
ABL1	ABL1_IMATI	IMATI	hinge	loop	kinase	3	0.54	0.43	N/A	N/A	0	in	other	True	in	in	False
ABL1	ABL1_IMATI	IMATI	hinge	loop	kinase	3	0.54	0.46	N/A	N/A	0	in	other	True	in	in	False
ABL1	ABL1_IMATI	IMATI	pocket_scaffold	loop	kinase	73	2.03	0.00	-146.00	-133.00	8	in	other	True	in	in	False
ABL1	ABL1_IMATI	IMATI	pocket_scaffold	loop	kinase	73	1.75	0.00	-146.00	-133.00	9	in	other	True	in	in	False
ABL1	ABL1_IMATI	IMATI	alphaC_Glu	point	kinase	1	1.51	1.51	N/A	N/A	0	in	other	True	in	in	False
ABL1	ABL1_IMATI	IMATI	alphaC_Glu	point	kinase	1	1.52	1.52	N/A	N/A	0	in	other	True	in	in	False
ABL1	ABL1_IMATI	IMATI	catalytic_Lys	point	kinase	1	1.41	1.41	N/A	N/A	0	in	other	True	in	in	False
ABL1	ABL1_IMATI	IMATI	catalytic_Lys	point	kinase	1	1.01	1.01	N/A	N/A	0	in	other	True	in	in	False
ABL1	ABL1_IMATI	IMATI	gatekeeper	point	kinase	1	0.35	0.35	N/A	N/A	0	in	other	True	in	in	False
ABL1	ABL1_IMATI	IMATI	gatekeeper	point	kinase	1	0.37	0.37	N/A	N/A	0	in	other	True	in	in	False

Download CSV

Family coverage and SSE shifts

Family	Status	Detail
ABL1	OK	28 motif row(s) across 4 target(s), annotator=kinase
ABLAP	No apo structure configured	No 'Apo structure:' configured for this family

Overall shift statistics

2 target(s), 28 motif(s) compared
Mean Ca RMSD: 1.32 A (median 0.89 A) — largest shift: 5.58 A at ABL1_IMATI / DFG
Mean centroid shift: 0.95 A
Flagged phi/psi outlier residues: 39
Kinase state changes detected: 21 DFG, 0 alphaC

Per-motif Ca RMSD

Loops

Transmembrane

Selectivity and motif shifts

Family x ligand selectivity

Motif x target RMSD

Ligand pose vs experiment

4 target(s) compared against experimental structures in reference/. Atoms are paired by molecular graph, so the symmetry of the ligand is respected rather than being resolved by whichever atom happened to be nearest.

Target	Protein	Ligand	Pocket	Reference	Site (A)	Pose (A)	Conformer (A)
ABL1_IMATI_1N1	ABL1	IMATI	1N1	1IEP (STI)	0.36	0.72	0.29
ABL1_IMATI	ABL1	IMATI	unconstrained	1IEP (STI)	0.38	1.31	0.75
ABL1_DASAT_1N1	ABL1	DASAT	1N1	2GQG (1N1)	0.17	1.85	1.72
ABL1_DASAT	ABL1	DASAT	unconstrained	2GQG (1N1)	0.96	2.22	1.70

🎯 site Same site (< 2 A) Nearby (2-5 A) Elsewhere (≥ 5 A)

pose Pose reproduced (< 2 A) Approximate (2-5 A) Different pose (≥ 5 A)

Predicted against experimental

Residue interaction fingerprints

Which residues each ligand touches, per protein. One scale for all of them, so a strong contact looks the same in every plot.

ABL1

The reports as files

The same panels as BoltzMaker wrote them, if you want the whole page in one file.

Full dashboard (8.0 MB) Secondary structure (apo vs holo) (4.4 MB)

Landlord narration

5 of 5 target summaries written on-device by the Apple Neural Engine; 0 rendered from the template. Every number here is checked against the figures the analysis computed; a summary stating one it was not given was replaced by the template.

This campaign predicted the binding affinity of five ligands to the ABL1 protein, with three of the five targets deemed to be of high potency, and two of the five targets deemed to be of moderate potency. Of the five predicted targets, two of the targets were flagged as carrying at least one flag, and these were deemed to be of moderate potency.

Targets	5 predicted, 4 with a ligand
Receptors	ABL1, ABLAP
Ligands	DASAT, IMATI
Verdicts	3 proceed, 2 caution
Confidence	5 well determined
Flagged	2 of 5
Pose validated	3 of 4 reproduced the experimental pose

Key findings

Of 5 targets, 3 are marked proceed, 2 caution and 0 discard.
5 of 5 targets are well determined; 0 are not.
2 of 5 targets carry at least one flag.
4 targets could be checked against an experimental structure, and 3 reproduced the experimental pose.

Highest predicted potency

DASAT on 4_ABL1_DASAT_1N1, predicted pIC50 12.86
IMATI on 2_ABL1_IMATI_1N1, predicted pIC50 10.1
DASAT on 3_ABL1_DASAT_Unc, predicted pIC50 9.89

Caveats

This campaign failed to flag any of the predicted targets as being of low or no potency. Furthermore, the predicted potency of the ligands may not be applicable to other ligands or conditions.

Per target

Target	Verdict	Summary	Caveat	Written by
`ABL1_IMATI`	caution	Well determined; this means that the structure is likely accurate and reliable for the intended use. IMATI is a control ligand with 17 contacts, including 10 hydrophobic contacts, 5 hydrogen bonds, and 2 salt bridges. Its predicted potency is 9.36, which places it at rank 4 out of 4 by predicted potency. The predicted potency varies widely across the ensemble, meaning that the predicted potency of IMATI may not be applicable to other ligands or conditions.	The predicted potency varies widely across the ensemble; this means that the predicted potency of IMATI may not be applicable to other ligands or conditions.	model
`ABL1_IMATI_1N1`	proceed	The structure is well determined, suggesting it is reliable for further study. IMATI is a control ligand with 16 contacts, 10 hydrophobic and 4 hydrogen bonds, and a predicted potency of 10.1. It is ranked 2 of 4 by predicted potency.	No flags were present, indicating no immediate concerns about the structure's validity.	model
`ABL1_DASAT`	proceed	This structure is well determined, meaning it is likely to be accurate. This is important for scientists who are deciding whether to trust this structure. DASAT is an inhibitor that binds to the target with 11 total contacts (8 hydrophobic and 3 hydrogen bonds). Its predicted potency is 9.89, and it ranks 3 out of 4 by predicted potency.	There are no flags indicating any issues with the structure.	model
`ABL1_DASAT_1N1`	proceed	This structure is well determined, and that means it should be trusted. DASAT is an inhibitor that binds to ABL1 with 7 hydrophobic contacts and 3 hydrogen bonds, and its predicted potency is 12.86 nM. Its predicted potency ranks it as the most potent inhibitor among four tested ligands.	There are no flags indicating problems with the structure. However, the predicted potency of the ligand is not very high, so it may not be a very potent inhibitor.	model
`ABLAP`	caution	This structure is well determined, but caution is still recommended.	The ligand is poorly placed relative to the receptor and interaction analysis did not complete for this target	model