FAIRMol

TC358

Pose ID 9058 Compound 44 Pose 250

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
T14
T. brucei ODC (G418 binding site) T. brucei G418 binding site
Ligand TC358
PDB1NJJ↗

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 mixed SASA done
Strain ΔE
30.9 kcal/mol
Protein clashes
0
Internal clashes
16
Native overlap
contact recall 0.53, Jaccard 0.36, H-bond role recall 0.20
Burial
70%
Hydrophobic fit
90%
Reason: 16 internal clashes
16 intramolecular clashes 46% of hydrophobic surface appears solvent-exposed (11/24 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 (-0.670 kcal/mol/HA) ✓ Good fit quality (FQ -6.46) ✓ Good H-bonds (5 bonds) ✓ Deep burial (70% SASA buried) ✓ Lipophilic contacts well-matched (90%) ✗ Very high strain energy (30.9 kcal/mol) ✗ Geometry warnings ✗ Many internal clashes (16)
Score
-20.101
kcal/mol
LE
-0.670
kcal/mol/HA
Fit Quality
-6.46
FQ (Leeson)
HAC
30
heavy atoms
MW
402
Da
LogP
3.56
cLogP
Strain ΔE
30.9 kcal/mol
SASA buried
70%
Lipo contact
90% BSA apolar/total
SASA unbound
677 Ų
Apolar buried
426 Ų

Interaction summary

HB 5 HY 7 PI 0 CLASH 0 ⚠ Exposure 45%

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.
⚠️Partial hydrophobic solvent exposure
46% of hydrophobic surface appears solvent-exposed (11/24 atoms). Partial exposure is common but may limit selectivity and membrane permeability.
Non-polar atoms 24 Buried (contacted) 13 Exposed 11 LogP 3.56 H-bonds 5
Exposed fragments: phenyl (2/5 atoms exposed)phenyl (6/6 atoms exposed)aliphatic chain/group (3 atoms exposed)
Final rank3.403Score-20.101
Inter norm-0.752Intra norm0.082
Top1000noExcludedno
Contacts15H-bonds5
Artifact reasongeometry warning; 16 clashes; 2 protein clashes; high strain Δ 30.3
Residues
ARG22 ARG342 ARG50 ASN20 ASP44 CYS26 GLN341 GLU343 GLU384 LEU25 LEU382 PRO340 PRO344 THR21 THR285

Native ligand reference

★ reference
Interaction fingerprint calculated directly from the uploaded native ligand without docking. Current H-bond mode: strict.
Name1NJJContacts15
PoseOpen native poseHB0
IFP residues
ARG22 ARG242 ARG337 ARG342 ASP243 ASP385 GLN341 GLU384 LEU25 LEU339 LEU382 PRO340 PRO344 SER282 THR241
Current overlap8Native recall0.53
Jaccard0.36RMSD-
HB strict1Strict recall0.17
HB same residue+role1HB role recall0.20
HB same residue1HB residue recall0.20

Protein summary

398 residues
Protein targetT14Atoms6140
Residues398Chains1
Residue summaryVAL:592; LEU:513; LYS:484; ARG:432; PHE:420; ILE:418; ASP:349; THR:322; TYR:315; PRO:308; GLU:301; ALA:290; SER:253; GLY:217; ASN:210; GLN:170

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:ORX602

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 0 0.00 0.00 - no Open
250 3.403056279509119 -0.752278 -20.1012 5 15 8 0.53 0.20 - no Current
277 3.748241609510073 -0.734284 -18.7968 5 12 0 0.00 0.00 - 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 -20.101kcal/mol
Ligand efficiency (LE) -0.6700kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -6.463
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) 30.89kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy 91.11kcal/mol
Minimised FF energy 60.22kcal/mol

SASA & burial

✓ computed
SASA (unbound) 676.9Ų
Total solvent-accessible surface area of free ligand
BSA total 471.9Ų
Buried surface area upon binding
BSA apolar 426.0Ų
Hydrophobic contacts buried
BSA polar 45.9Ų
Polar contacts buried
Fraction buried 69.7%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 90.3%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -2587.7Ų
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 3349.0Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA 1388.8Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)