FAIRMol

TC487

Pose ID 11112 Compound 352 Pose 269

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
T17
T. brucei TR (Doorstop site) T. brucei Doorstop site
Ligand TC487
PDB5S9T↗

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 high Native strong SASA done
Strain ΔE
22.9 kcal/mol
Protein clashes
1
Internal clashes
1
Native overlap
contact recall 0.83, Jaccard 0.50, H-bond role recall 1.00
Burial
74%
Hydrophobic fit
79%
Reason: no major geometry red flags detected
1 protein-contact clashes 64% of hydrophobic surface is solvent-exposed (14/22 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 (-0.664 kcal/mol/HA) ✓ Good fit quality (FQ -6.41) ✓ Strong H-bond network (7 bonds) ✓ Deep burial (74% SASA buried) ✓ Lipophilic contacts well-matched (79%) ✗ High strain energy (22.9 kcal/mol) ✗ Geometry warnings ✗ Many internal clashes (12)
Score
-19.923
kcal/mol
LE
-0.664
kcal/mol/HA
Fit Quality
-6.41
FQ (Leeson)
HAC
30
heavy atoms
MW
428
Da
LogP
3.96
cLogP
Strain ΔE
22.9 kcal/mol
SASA buried
74%
Lipo contact
79% BSA apolar/total
SASA unbound
691 Ų
Apolar buried
402 Ų

Interaction summary

HB 7 HY 7 PI 1 CLASH 1 ⚠ Exposure 63%

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

PI · π–π interactions
Native π–π recall is disabled because no explicit native π–π reference was stored.

HY · Hydrophobic contacts

CLASH · Clashes
🚨Solvent-exposed hydrophobic surface — desolvation penalty likely
64% of hydrophobic surface is solvent-exposed (14/22 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 22 Buried (contacted) 8 Exposed 14 LogP 3.96 H-bonds 7
Exposed fragments: phenyl (4/6 atoms exposed)phenyl (6/6 atoms exposed)aliphatic chain/group (4 atoms exposed)
Final rank4.602Score-19.923
Inter norm-0.783Intra norm0.119
Top1000noExcludedno
Contacts18H-bonds7
Artifact reasongeometry warning; 12 clashes; 3 protein clashes; moderate strain Δ 22.9
Residues
ALA363 ARG228 ARG331 CYS375 GLY197 GLY229 GLY376 HIS428 ILE378 LEU227 LEU332 LEU334 MET333 PHE198 PHE230 SER364 THR374 VAL362

Native ligand reference

★ reference
Interaction fingerprint calculated directly from the uploaded native ligand without docking. Current H-bond mode: strict.
Name5S9TContacts12
PoseOpen native poseHB0
IFP residues
ALA365 ARG228 ARG331 GLY229 LEU332 LEU334 MET333 PHE198 PHE230 SER364 THR374 VAL366
Current overlap10Native recall0.83
Jaccard0.50RMSD-
HB strict1Strict recall1.00
HB same residue+role1HB role recall1.00
HB same residue1HB residue recall1.00

Protein summary

1033 residues
Protein targetT17Atoms15160
Residues1033Chains2
Residue summaryVAL:1536; LEU:1387; LYS:1386; ILE:1064; GLU:900; THR:868; ARG:816; PHE:800; ALA:780; ASN:700; PRO:686; GLY:672; SER:616; TYR:588; ASP:528; MET:408

Receptor context

2 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 2 Excluded HETATM 0
Kept cofactors / ions
A:FAD501 B: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 0 0.00 0.00 - no Open
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 10 0.83 1.00 - no Current
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 -19.923kcal/mol
Ligand efficiency (LE) -0.6641kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -6.406
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) 22.93kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy 82.50kcal/mol
Minimised FF energy 59.56kcal/mol

SASA & burial

✓ computed
SASA (unbound) 691.2Ų
Total solvent-accessible surface area of free ligand
BSA total 510.0Ų
Buried surface area upon binding
BSA apolar 402.3Ų
Hydrophobic contacts buried
BSA polar 107.7Ų
Polar contacts buried
Fraction buried 73.8%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 78.9%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -6539.0Ų
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 8063.1Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA 2078.0Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)