FAIRMol

TC391

Pose ID 10502 Compound 477 Pose 337

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
T16
T. brucei TR (Dimer interface (site 2)) T. brucei Dimer interface (site 2)
Ligand TC391
PDB6RB5↗

3D complex viewer

Receptor not available — ligand geometry only, interactions disabled.
Strict H-bonds Permissive H-bonds
Viewer legend
Protein receptor
Pocket residues
Cofactor context
Docked ligand
Overall assessment
Weak SASA cached
Promising but geometrically suspicious
Binding strong Geometry low Native mixed SASA done
Strain ΔE
20.5 kcal/mol
Protein clashes
0
Internal clashes
12
Native overlap
contact recall 0.42, Jaccard 0.25
Burial
71%
Hydrophobic fit
77%
Reason: 12 internal clashes
12 intramolecular clashes 100% of hydrophobic surface is solvent-exposed (23/23 atoms). Large non-polar area without protein contacts incurs a desolvation penalty and will reduce binding affinity. Consider truncating or replacing the exposed fragment.
Molecular report
Full metrics ↗
Weak Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-0.716 kcal/mol/HA) ✓ Good fit quality (FQ -6.91) ✓ Deep burial (71% SASA buried) ✓ Lipophilic contacts well-matched (77%) ✗ High strain energy (20.5 kcal/mol) ✗ No H-bonds detected ✗ Geometry warnings ✗ Many internal clashes (12)
Score
-21.483
kcal/mol
LE
-0.716
kcal/mol/HA
Fit Quality
-6.91
FQ (Leeson)
HAC
30
heavy atoms
MW
428
Da
LogP
4.90
cLogP
Strain ΔE
20.5 kcal/mol
SASA buried
71%
Lipo contact
77% BSA apolar/total
SASA unbound
686 Ų
Apolar buried
375 Ų

Interaction summary

HB 0 HY 0 PI 0 CLASH 0 ⚠ Exposure 100%
🚨Solvent-exposed hydrophobic surface — desolvation penalty likely
100% of hydrophobic surface is solvent-exposed (23/23 atoms). Large non-polar area without protein contacts incurs a desolvation penalty and will reduce binding affinity. Consider truncating or replacing the exposed fragment.
Non-polar atoms 23 Buried (contacted) 0 Exposed 23 LogP 4.9 H-bonds 0
Exposed fragments: phenyl (6/6 atoms exposed)phenyl (4/6 atoms exposed)phenyl (3/5 atoms exposed)phenyl (6/6 atoms exposed)aliphatic chain/group (6 atoms exposed)
Final rank4.126Score-21.483
Inter norm-0.761Intra norm0.045
Top1000noExcludedno
Contacts13H-bonds7
Artifact reasongeometry warning; 12 clashes; 3 protein clashes
Residues
ALA209 ALA90 ASN91 GLY214 GLY215 LYS211 LYS89 LYS93 PRO187 PRO212 PRO213 TRP92 VAL88

Protein summary

493 residues
Protein targetT16Atoms7551
Residues493Chains1
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:276; MET:221

Native ligand reference

★ reference
Interaction fingerprint calculated directly from the uploaded native ligand without docking. Current H-bond mode: strict.
Name6RB5Contacts12
PoseOpen native poseHB0
IFP residues
ALA90 ARG74 GLY85 LEU73 LYS89 MET70 PHE83 PRO212 PRO213 SER86 SER87 VAL88
Current overlap5Native recall0.42
Jaccard0.25RMSD-
HB strict0Strict recall-
HB same residue+role0HB role recall-
HB same residue0HB residue recall-

HB · H-bonds
No hb · h-bonds detected for this pose.

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

HY · Hydrophobic contacts
No hy · hydrophobic contacts detected for this pose.

CLASH · Clashes
No clash · clashes detected for this pose.

All stored poses for this docking hit

PoseFinal rankInter normScoreHBCTCT overlapCT recallHB role rec.RMSDExcluded
232 1.8331583620386547 -1.27971 -26.7454 4 18 0 0.00 - - no Open
280 2.0200071560901884 -0.858313 -23.3297 3 18 0 0.00 - - no Open
274 2.045457668570819 -0.972567 -23.9357 6 14 1 0.08 - - no Open
166 2.6403647932585232 -0.945898 -27.3365 11 17 0 0.00 - - no Open
252 2.7011556067534275 -0.828299 -17.981 8 15 0 0.00 - - no Open
301 2.747981289497286 -0.894508 -23.189 4 18 0 0.00 - - no Open
164 2.7801382971405904 -0.980978 -23.9123 8 18 0 0.00 - - no Open
259 2.982627401034303 -0.855249 -21.6476 7 16 0 0.00 - - no Open
365 3.608801145484245 -0.888327 -22.7927 5 16 0 0.00 - - no Open
221 3.673195067444817 -1.01885 -23.2926 9 17 0 0.00 - - no Open
198 3.840362266733292 -0.951165 -20.9586 6 18 0 0.00 - - no Open
337 4.12591610565581 -0.761025 -21.4826 7 13 5 0.42 - - no Current
183 4.337579311682156 -1.02771 -24.7008 7 20 0 0.00 - - no Open
221 4.478220481332508 -1.00163 -22.7724 5 19 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 -21.483kcal/mol
Ligand efficiency (LE) -0.7161kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -6.908
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 30HA

Physicochemical properties
Molecular weight 427.5Da
Lipinski: ≤ 500 Da
LogP (cLogP) 4.90
Lipinski: ≤ 5
Rotatable bonds 7

Conformational strain (MMFF94s)
Strain energy (ΔE) 20.54kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy 76.60kcal/mol
Minimised FF energy 56.07kcal/mol

SASA & burial

✓ computed
SASA (unbound) 686.1Ų
Total solvent-accessible surface area of free ligand
BSA total 489.8Ų
Buried surface area upon binding
BSA apolar 375.3Ų
Hydrophobic contacts buried
BSA polar 114.4Ų
Polar contacts buried
Fraction buried 71.4%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 76.6%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -3159.2Ų
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 4076.6Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA 1472.3Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)