FAIRMol

NMT-TY0569

Pose ID 13869 Compound 1590 Pose 311

DB fairmolDocking pose analysis is being read from this database.
Compound detail Protein structures Back to compounds
Molecular metrics status: done
RDKit SASA-based burial metrics are cached.
SASA cached
T21
T. cruzi R5P T. cruzi
Ligand NMT-TY0569
PDB3K7O↗

3D complex viewer

Strict H-bonds Permissive H-bonds
Viewer legend
Protein receptor
Pocket residues
Cofactor context
Docked ligand
Overall assessment
Weak SASA cached
Weak or marginal quality
Binding strong Geometry medium Native strong SASA done
Strain ΔE
19.8 kcal/mol
Protein clashes
3
Internal clashes
3
Native overlap
contact recall 1.00, Jaccard 0.78, H-bond role recall 0.56
Burial
87%
Hydrophobic fit
57%
Reason: no major geometry red flags detected
3 protein-contact clashes 3 intramolecular clashes
EcoTox / ADMET In-silico prediction only
Fish LC₅₀
Not classified (>100 mg/L)
Daphnia EC₅₀
Not classified (>100 mg/L)
Algae IC₅₀
Not classified (>100 mg/L)
Bioaccum.
Not B (BCF≤2000)
Persistent
No
ADMET alerts (in-silico)
hERG Low Ames Clear DILI Low
Molecular report
Full metrics ↗
Weak Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-1.098 kcal/mol/HA) ✓ Good fit quality (FQ -9.53) ✓ Strong H-bond network (9 bonds) ✓ Deep burial (87% SASA buried) ✗ Moderate strain (19.8 kcal/mol) ✗ Geometry warnings ✗ Many internal clashes (10)
Score
-24.154
kcal/mol
LE
-1.098
kcal/mol/HA
Fit Quality
-9.53
FQ (Leeson)
HAC
22
heavy atoms
MW
324
Da
LogP
-0.18
cLogP
Final rank
3.4069
rank score
Inter norm
-1.131
normalised
Contacts
18
H-bonds 13
Strain ΔE
19.8 kcal/mol
SASA buried
87%
Lipo contact
57% BSA apolar/total
SASA unbound
507 Ų
Apolar buried
250 Ų

Interaction summary

HBD 2 HBA 7 HY 4 PI 3 CLASH 3

HBD/HBA · H-bonds (geometric)
HBD = ligand donates H · HBA = ligand accepts H · ~ = weak (≥110°). Mode: strict. Residues: 6.

PI · π–π interactions
Native π–π recall is disabled because no explicit native π–π reference was stored.

HY · Hydrophobic contacts

CLASH · Clashes

Native ligand reference

★ reference
Interaction fingerprint calculated directly from the uploaded native ligand without docking. Current H-bond mode: strict.
Name3K7OContacts14
PoseOpen native poseHB0
IFP residues
ARG137 ARG141 ASN103 HIS102 HIS138 ASP10 CYS69 GLY70 GLY74 HIS11 ILE73 PRO12 SER71 TYR46
Current overlap14Native recall1.00
Jaccard0.78RMSD-
HB strict6Strict recall0.50
HB same residue+role5HB role recall0.56
HB same residue5HB residue recall0.62

Protein summary

305 residues
Protein targetT21Atoms4646
Residues305Chains2
Residue summaryARG:576; ILE:532; VAL:512; GLU:420; ALA:360; PHE:240; HIS:238; LYS:220; THR:210; LEU:190; PRO:168; TYR:168; GLY:154; SER:154; ASP:144; ASN:112

All stored poses for this docking hit

PoseFinal rankInter normScoreHBCTCT overlapCT recallHB role rec.RMSDExcluded
314 0.006401770887810909 -1.242 -25.2095 8 12 0 0.00 0.00 - no Open
279 3.0034143639523716 -1.39924 -29.4385 16 19 0 0.00 0.00 - no Open
311 3.4068605407179655 -1.13086 -24.1545 13 18 14 1.00 0.56 - no Current
251 5.16877485116465 -1.26971 -25.2723 12 16 0 0.00 0.00 - no Open

Molecular metrics

RDKit SASA burial, strain energy (MMFF94s), ligand efficiency and fit quality for this docking pose.
✓ Metrics available

Scoring & efficiency
Docking score -24.154kcal/mol
Ligand efficiency (LE) -1.0979kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -9.532
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 22HA

Physicochemical properties
Molecular weight 324.3Da
Lipinski: ≤ 500 Da
LogP (cLogP) -0.18
Lipinski: ≤ 5
Rotatable bonds 4

Conformational strain (MMFF94s)
Strain energy (ΔE) 19.76kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy -122.05kcal/mol
Minimised FF energy -141.81kcal/mol

SASA & burial

✓ computed
SASA (unbound) 507.4Ų
Total solvent-accessible surface area of free ligand
BSA total 439.8Ų
Buried surface area upon binding
BSA apolar 250.4Ų
Hydrophobic contacts buried
BSA polar 189.4Ų
Polar contacts buried
Fraction buried 86.7%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 56.9%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -2034.9Ų
SASA_nonpolar(complex) − SASA_nonpolar(receptor) − SASA_nonpolar(ligand free). Negative = non-polar surface buried upon binding. Requires full polarity-decomposed SASA computation.
Receptor non-polar SASA 2482.0Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA 742.2Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)