FAIRMol

TC487

Pose ID 13166 Compound 352 Pose 287

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
T20
T. brucei TR (Z-site (fragment hotspot)) T. brucei Z-site (fragment hotspot)
Ligand TC487
PDB9IFH↗

3D complex viewer

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 strong SASA done
Strain ΔE
38.6 kcal/mol
Protein clashes
0
Internal clashes
14
Native overlap
contact recall 0.75, Jaccard 0.43, H-bond role recall 0.00
Burial
61%
Hydrophobic fit
78%
Reason: 14 internal clashes
14 intramolecular clashes
Molecular report
Full metrics ↗
Weak Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-0.490 kcal/mol/HA) ✓ Good fit quality (FQ -4.73) ✓ Good H-bonds (5 bonds) ✓ Good burial (61% SASA buried) ✓ Lipophilic contacts well-matched (78%) ✗ Very high strain energy (38.6 kcal/mol) ✗ Geometry warnings ✗ Many internal clashes (14)
Score
-14.700
kcal/mol
LE
-0.490
kcal/mol/HA
Fit Quality
-4.73
FQ (Leeson)
HAC
30
heavy atoms
MW
428
Da
LogP
3.96
cLogP
Strain ΔE
38.6 kcal/mol
SASA buried
61%
Lipo contact
78% BSA apolar/total
SASA unbound
687 Ų
Apolar buried
328 Ų

Interaction summary

HB 5 HY 16 PI 0 CLASH 0

HB · H-bonds
Mode: strict. Count shows atom-level H-bonds; unique residues in summary: 0.

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

HY · Hydrophobic contacts

CLASH · Clashes
No clash · clashes detected for this pose.
Final rank3.837Score-14.700
Inter norm-0.648Intra norm0.157
Top1000noExcludedno
Contacts12H-bonds5
Artifact reasongeometry warning; 14 clashes; 2 protein clashes; high strain Δ 38.6
Residues
ASN402 GLU466 GLU467 HIS461 LEU399 MET400 PHE396 PRO398 PRO462 SER464 THR397 THR463

Native ligand reference

★ reference
Interaction fingerprint calculated directly from the uploaded native ligand without docking. Current H-bond mode: strict.
Name9IFHContacts8
PoseOpen native poseHB0
IFP residues
ASN402 GLU467 LEU399 PHE396 PRO398 SER394 SER470 THR397
Current overlap6Native recall0.75
Jaccard0.43RMSD-
HB strict0Strict recall0.00
HB same residue+role0HB role recall0.00
HB same residue0HB residue recall0.00

Protein summary

492 residues
Protein targetT20Atoms7539
Residues492Chains1
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:221

Receptor context

1 kept / 0 excluded
Receptor context filtering: interactions and SASA are computed against protein atoms plus allowed cofactors/ions. Native ligand-like HETATM partners are excluded from scoring.
Kept context 1 Excluded HETATM 0
Kept cofactors / ions
A:FAD501

All stored poses for this docking hit

PoseFinal rankInter normScoreHBCTCT overlapCT recallHB role rec.RMSDExcluded
290 0.8017311614907171 -0.908661 -23.0929 6 19 0 0.00 0.00 - no Open
289 1.1891934264856294 -0.986427 -25.4869 6 10 0 0.00 0.00 - no Open
226 1.5612750493986565 -0.771977 -19.4826 3 19 0 0.00 0.00 - no Open
300 2.1179682723188282 -0.934578 -22.8791 6 18 0 0.00 0.00 - no Open
262 2.399824276567599 -0.752579 -21.269 5 15 0 0.00 0.00 - no Open
209 3.0410827936045286 -0.975088 -25.9209 4 18 0 0.00 0.00 - no Open
248 3.1462562544506847 -0.786482 -20.8151 5 15 0 0.00 0.00 - no Open
251 3.320904741573509 -0.887126 -22.6215 10 12 0 0.00 0.00 - no Open
163 3.477429104976751 -1.00816 -23.4165 10 19 0 0.00 0.00 - no Open
287 3.836641570962658 -0.64787 -14.6997 5 12 6 0.75 0.00 - no Current
175 4.216104188406848 -1.04114 -29.1927 13 17 0 0.00 0.00 - no Open
269 4.601908702211421 -0.782747 -19.9233 7 18 0 0.00 0.00 - no Open
239 5.345105059884922 -0.932927 -25.0434 12 17 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 -14.700kcal/mol
Ligand efficiency (LE) -0.4900kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -4.727
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 30HA

Physicochemical properties
Molecular weight 427.5Da
Lipinski: ≤ 500 Da
LogP (cLogP) 3.96
Lipinski: ≤ 5
Rotatable bonds 7

Conformational strain (MMFF94s)
Strain energy (ΔE) 38.61kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy 98.23kcal/mol
Minimised FF energy 59.62kcal/mol

SASA & burial

✓ computed
SASA (unbound) 686.7Ų
Total solvent-accessible surface area of free ligand
BSA total 420.1Ų
Buried surface area upon binding
BSA apolar 327.7Ų
Hydrophobic contacts buried
BSA polar 92.4Ų
Polar contacts buried
Fraction buried 61.2%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 78.0%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -3133.6Ų
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 4069.8Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA 1502.2Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)