FAIRMol

NMT-TY0429

Pose ID 13859 Compound 4011 Pose 301

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-TY0429
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
35.4 kcal/mol
Protein clashes
2
Internal clashes
2
Native overlap
contact recall 0.71, Jaccard 0.56, H-bond role recall 0.56
Burial
85%
Hydrophobic fit
66%
Reason: no major geometry red flags detected
2 protein-contact 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 (-1.415 kcal/mol/HA) ✓ Good fit quality (FQ -11.07) ✓ Strong H-bond network (8 bonds) ✓ Deep burial (85% SASA buried) ✓ Lipophilic contacts well-matched (66%) ✗ Very high strain energy (35.4 kcal/mol) ✗ Geometry warnings ✗ Internal clashes (7)
Score
-24.062
kcal/mol
LE
-1.415
kcal/mol/HA
Fit Quality
-11.07
FQ (Leeson)
HAC
17
heavy atoms
MW
256
Da
LogP
-0.39
cLogP
Final rank
1.8144
rank score
Inter norm
-1.459
normalised
Contacts
14
H-bonds 10
Strain ΔE
35.4 kcal/mol
SASA buried
85%
Lipo contact
66% BSA apolar/total
SASA unbound
453 Ų
Apolar buried
254 Ų

Interaction summary

HBD 4 HBA 4 HY 4 PI 1 CLASH 2

HBD/HBA · H-bonds (geometric)
HBD = ligand donates H · HBA = ligand accepts H · ~ = weak (≥110°). Mode: permissive. 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: permissive.
Name3K7OContacts14
PoseOpen native poseHB0
IFP residues
ARG137 ARG141 ASN103 HIS102 HIS138 ASP10 CYS69 GLY70 GLY74 HIS11 ILE73 PRO12 SER71 TYR46
Current overlap10Native recall0.71
Jaccard0.56RMSD-
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
301 1.8144453480802607 -1.45928 -24.0617 10 14 10 0.71 0.56 - no Current
232 3.3143497304329887 -1.78781 -27.6033 16 18 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 -24.062kcal/mol
Ligand efficiency (LE) -1.4154kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -11.068
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 17HA

Physicochemical properties
Molecular weight 256.3Da
Lipinski: ≤ 500 Da
LogP (cLogP) -0.39
Lipinski: ≤ 5
Rotatable bonds 3

Conformational strain (MMFF94s)
Strain energy (ΔE) 35.40kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy -66.06kcal/mol
Minimised FF energy -101.46kcal/mol

SASA & burial

✓ computed
SASA (unbound) 452.8Ų
Total solvent-accessible surface area of free ligand
BSA total 384.5Ų
Buried surface area upon binding
BSA apolar 254.4Ų
Hydrophobic contacts buried
BSA polar 130.1Ų
Polar contacts buried
Fraction buried 84.9%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 66.2%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -2036.0Ų
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 747.1Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)