FAIRMol

OHD_TbNat_104

Pose ID 9552 Compound 579 Pose 66

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
T15
T. brucei TR (Dimer cleft site) T. brucei Dimer cleft site
Ligand OHD_TbNat_104
PDB9IFF↗

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
33.5 kcal/mol
Protein clashes
3
Internal clashes
3
Native overlap
contact recall 0.69, Jaccard 0.47
Burial
75%
Hydrophobic fit
65%
Reason: no major geometry red flags detected
3 protein-contact clashes 3 intramolecular clashes 43% of hydrophobic surface appears solvent-exposed (9/21 atoms). Partial exposure is common but may limit selectivity and membrane permeability.
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 Alert DILI Low
Molecular report
Full metrics ↗
Weak Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-0.660 kcal/mol/HA) ✓ Good fit quality (FQ -6.43) ✓ Good H-bonds (5 bonds) ✓ Deep burial (75% SASA buried) ✓ Lipophilic contacts well-matched (65%) ✗ Very high strain energy (33.5 kcal/mol) ✗ Geometry warnings ✗ Many internal clashes (11)
Score
-20.476
kcal/mol
LE
-0.660
kcal/mol/HA
Fit Quality
-6.43
FQ (Leeson)
HAC
31
heavy atoms
MW
436
Da
LogP
-0.56
cLogP
Final rank
4.6892
rank score
Inter norm
-0.774
normalised
Contacts
15
H-bonds 10
Strain ΔE
33.5 kcal/mol
SASA buried
75%
Lipo contact
65% BSA apolar/total
SASA unbound
665 Ų
Apolar buried
326 Ų

Interaction summary

HBD 2 HBA 3 HY 5 PI 0 CLASH 3

HBD/HBA · H-bonds (geometric)
HBD = ligand donates H · HBA = ligand accepts H · ~ = weak (≥110°). Mode: permissive. 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: permissive.
Name9IFFContacts13
PoseOpen native poseHB0
IFP residues
ALA209 ARG74 ASN208 GLY214 GLY215 GLY85 LEU73 LYS211 MET70 PHE83 PRO212 PRO213 VAL88
Current overlap9Native recall0.69
Jaccard0.47RMSD-
HB strict0Strict recall-
HB same residue+role0HB role recall-
HB same residue0HB residue recall-

Protein summary

489 residues
Protein targetT15Atoms7420
Residues489Chains1
Residue summaryVAL:768; LYS:704; LEU:703; ILE:532; GLU:450; THR:434; ARG:408; PHE:400; ALA:390; ASN:350; PRO:350; GLY:336; SER:319; TYR:294; ASP:264; MET:204

All stored poses for this docking hit

PoseFinal rankInter normScoreHBCTCT overlapCT recallHB role rec.RMSDExcluded
84 1.0179927732673884 -1.02326 -25.6202 10 15 0 0.00 - - no Open
87 3.2642859531252832 -0.996734 -27.8364 12 13 0 0.00 - - no Open
86 3.3606023215307887 -0.929678 -30.7755 8 21 0 0.00 - - no Open
94 3.411734690087445 -0.925891 -27.3176 9 21 0 0.00 - - no Open
66 3.4554389482171013 -0.84221 -25.2275 7 15 0 0.00 - - no Open
83 4.060877043540257 -0.820497 -20.7829 8 18 0 0.00 - - no Open
81 4.253628773031853 -0.609689 -21.6506 7 10 0 0.00 - - no Open
66 4.689246763870224 -0.774342 -20.4763 10 15 9 0.69 - - no Current
45 5.218613317744509 -0.936281 -18.0731 14 18 0 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 -20.476kcal/mol
Ligand efficiency (LE) -0.6605kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -6.435
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 31HA

Physicochemical properties
Molecular weight 436.4Da
Lipinski: ≤ 500 Da
LogP (cLogP) -0.56
Lipinski: ≤ 5
Rotatable bonds 10

Conformational strain (MMFF94s)
Strain energy (ΔE) 33.50kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy 177.23kcal/mol
Minimised FF energy 143.73kcal/mol

SASA & burial

✓ computed
SASA (unbound) 665.5Ų
Total solvent-accessible surface area of free ligand
BSA total 499.4Ų
Buried surface area upon binding
BSA apolar 325.7Ų
Hydrophobic contacts buried
BSA polar 173.7Ų
Polar contacts buried
Fraction buried 75.0%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 65.2%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -2940.0Ų
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 4005.2Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA 1527.8Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)