FAIRMol

OHD_TbNat_71

Pose ID 13609 Compound 4212 Pose 51

DB SELECTIONDocking 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 OHD_TbNat_71
PDB3K7O↗

3D complex viewer

Strict H-bonds Permissive H-bonds
Viewer legend
Protein receptor
Pocket residues
Cofactor context
Docked ligand
Overall assessment
Reject SASA cached
Promising but geometrically suspicious
Binding strong Geometry low Native strong SASA done
Strain ΔE
43.1 kcal/mol
Protein clashes
3
Internal clashes
3
Native overlap
contact recall 1.00, Jaccard 0.82, H-bond role recall 0.56
Burial
67%
Hydrophobic fit
78%
Reason: strain 43.1 kcal/mol
strain ΔE 43.1 kcal/mol 3 protein-contact clashes 3 intramolecular clashes 60% of hydrophobic surface is solvent-exposed (18/30 atoms). Large non-polar area without protein contacts incurs a desolvation penalty and will reduce binding affinity. Consider truncating or replacing the exposed fragment.
EcoTox / ADMET In-silico prediction only
Fish LC₅₀
Cat. 2 — Toxic (1–10 mg/L)
Daphnia EC₅₀
Cat. 2 — Toxic (1–10 mg/L)
Algae IC₅₀
Cat. 2 — Toxic (1–10 mg/L)
Bioaccum.
Not B (BCF≤2000)
Persistent
No
ADMET alerts (in-silico)
hERG Low Ames Clear DILI Risk
Molecular report
Full metrics ↗
Reject Multiple quality flags — this pose should be deprioritised or discarded.
✓ Excellent LE (-0.491 kcal/mol/HA) ✓ Good fit quality (FQ -4.99) ✓ Good H-bonds (5 bonds) ✓ Deep burial (67% SASA buried) ✓ Lipophilic contacts well-matched (78%) ✗ Extreme strain energy (43.1 kcal/mol) ✗ Geometry warnings ✗ Internal clashes (7)
Score
-17.663
kcal/mol
LE
-0.491
kcal/mol/HA
Fit Quality
-4.99
FQ (Leeson)
HAC
36
heavy atoms
MW
505
Da
LogP
4.00
cLogP
Final rank
4.3578
rank score
Inter norm
-0.674
normalised
Contacts
17
H-bonds 7
Strain ΔE
43.1 kcal/mol
SASA buried
67%
Lipo contact
78% BSA apolar/total
SASA unbound
690 Ų
Apolar buried
358 Ų

Interaction summary

HBA 5 HY 3 PI 0 CLASH 3

HBD/HBA · H-bonds (geometric)
HBD = ligand donates H · HBA = ligand accepts H · ~ = weak (≥110°). Mode: strict. Residues: 4.

PI · π–π interactions
No pi · π–π interactions detected for this pose.

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
Jaccard0.82RMSD-
HB strict5Strict recall0.42
HB same residue+role5HB role recall0.56
HB same residue4HB residue recall0.50

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
80 3.1615656920501407 -0.642718 -23.3512 8 19 0 0.00 0.00 - no Open
84 3.6718129492115383 -0.652957 -20.6934 8 14 0 0.00 0.00 - no Open
51 4.357810901499544 -0.673922 -17.6629 7 17 14 1.00 0.56 - no Current

Molecular metrics

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

Scoring & efficiency
Docking score -17.663kcal/mol
Ligand efficiency (LE) -0.4906kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -4.987
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 36HA

Physicochemical properties
Molecular weight 504.7Da
Lipinski: ≤ 500 Da
LogP (cLogP) 4.00
Lipinski: ≤ 5
Rotatable bonds 6

Conformational strain (MMFF94s)
Strain energy (ΔE) 43.11kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy 139.05kcal/mol
Minimised FF energy 95.94kcal/mol

SASA & burial

✓ computed
SASA (unbound) 690.4Ų
Total solvent-accessible surface area of free ligand
BSA total 459.5Ų
Buried surface area upon binding
BSA apolar 358.0Ų
Hydrophobic contacts buried
BSA polar 101.5Ų
Polar contacts buried
Fraction buried 66.6%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 77.9%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -2296.7Ų
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 746.3Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)