FAIRMol

TC358

Pose ID 13155 Compound 44 Pose 276

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
T20
T. brucei TR (Z-site (fragment hotspot)) T. brucei Z-site (fragment hotspot)
Ligand TC358
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
Weak or marginal quality
Binding strong Geometry medium Native strong SASA done
Strain ΔE
30.6 kcal/mol
Protein clashes
1
Internal clashes
1
Native overlap
contact recall 0.75, Jaccard 0.50, H-bond role recall 1.00
Burial
53%
Hydrophobic fit
87%
Reason: no major geometry red flags detected
1 protein-contact clashes 38% of hydrophobic surface appears solvent-exposed (9/24 atoms). Partial exposure is common but may limit selectivity and membrane permeability.
Molecular report
Full metrics ↗
Weak Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-0.450 kcal/mol/HA) ✓ Good fit quality (FQ -4.34) ✓ Good H-bonds (5 bonds) ✓ Good burial (53% SASA buried) ✓ Lipophilic contacts well-matched (87%) ✗ Very high strain energy (30.6 kcal/mol) ✗ Geometry warnings ✗ Many internal clashes (11)
Score
-13.484
kcal/mol
LE
-0.450
kcal/mol/HA
Fit Quality
-4.34
FQ (Leeson)
HAC
30
heavy atoms
MW
402
Da
LogP
3.56
cLogP
Strain ΔE
30.6 kcal/mol
SASA buried
53%
Lipo contact
87% BSA apolar/total
SASA unbound
728 Ų
Apolar buried
332 Ų

Interaction summary

HB 5 HY 12 PI 1 CLASH 1 ⚠ Exposure 37%
⚠️Partial hydrophobic solvent exposure
38% of hydrophobic surface appears solvent-exposed (9/24 atoms). Partial exposure is common but may limit selectivity and membrane permeability.
Non-polar atoms 24 Buried (contacted) 15 Exposed 9 LogP 3.56 H-bonds 5
Exposed fragments: phenyl (6/6 atoms exposed)aliphatic chain/group (3 atoms exposed)
Final rank3.365Score-13.484
Inter norm-0.679Intra norm0.230
Top1000noExcludedno
Contacts10H-bonds5
Artifact reasongeometry warning; 11 clashes; 2 protein clashes; high strain Δ 30.6
Residues
ASN402 GLU466 GLU467 LEU399 LYS407 PHE396 PRO398 SER464 THR397 THR463

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

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
Jaccard0.50RMSD-
HB strict1Strict recall0.50
HB same residue+role1HB role recall1.00
HB same residue1HB residue recall1.00

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

All stored poses for this docking hit

PoseFinal rankInter normScoreHBCTCT overlapCT recallHB role rec.RMSDExcluded
230 0.5079880905865612 -1.05823 -27.4761 7 16 0 0.00 0.00 - no Open
299 0.6541166288479228 -0.854458 -23.1766 4 15 0 0.00 0.00 - no Open
235 0.9617741215431999 -1.12463 -25.229 6 14 0 0.00 0.00 - no Open
231 2.18855395233315 -0.988386 -20.5952 6 18 0 0.00 0.00 - no Open
229 2.2323899897137838 -1.22394 -27.7163 4 18 0 0.00 0.00 - no Open
218 2.2689055911488274 -0.78972 -23.284 2 18 0 0.00 0.00 - no Open
259 2.2729413366463573 -1.11623 -28.5408 6 22 0 0.00 0.00 - no Open
272 2.457874472716344 -0.902589 -22.2336 4 14 0 0.00 0.00 - no Open
177 2.6921673697430357 -0.935706 -23.0441 7 17 0 0.00 0.00 - no Open
260 3.0169256640293716 -1.16386 -28.6068 6 23 0 0.00 0.00 - no Open
210 3.164995907995662 -1.27123 -28.8488 8 23 0 0.00 0.00 - no Open
276 3.36488331222722 -0.679093 -13.4836 5 10 6 0.75 1.00 - no Current
250 3.403056279509119 -0.752278 -20.1012 5 15 0 0.00 0.00 - no Open
277 3.748241609510073 -0.734284 -18.7968 5 12 7 0.88 1.00 - no Open
363 4.041594586258085 -0.824173 -18.2023 6 18 0 0.00 0.00 - no Open
209 4.429054136335406 -1.09718 -26.8529 8 22 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 -13.484kcal/mol
Ligand efficiency (LE) -0.4495kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -4.336
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 30HA

Physicochemical properties
Molecular weight 402.5Da
Lipinski: ≤ 500 Da
LogP (cLogP) 3.56
Lipinski: ≤ 5
Rotatable bonds 10

Conformational strain (MMFF94s)
Strain energy (ΔE) 30.63kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy 89.25kcal/mol
Minimised FF energy 58.63kcal/mol

SASA & burial

✓ computed
SASA (unbound) 728.4Ų
Total solvent-accessible surface area of free ligand
BSA total 383.4Ų
Buried surface area upon binding
BSA apolar 332.1Ų
Hydrophobic contacts buried
BSA polar 51.4Ų
Polar contacts buried
Fraction buried 52.6%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 86.6%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -3196.2Ų
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 4069.8Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA 1537.3Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)