FAIRMol

TC393

Pose ID 9062 Compound 312 Pose 254

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 TC393
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
23.7 kcal/mol
Protein clashes
0
Internal clashes
15
Native overlap
contact recall 0.53, Jaccard 0.40, H-bond role recall 0.40
Burial
72%
Hydrophobic fit
84%
Reason: 15 internal clashes
15 intramolecular clashes 67% of hydrophobic surface is solvent-exposed (16/24 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 (-0.589 kcal/mol/HA) ✓ Good fit quality (FQ -5.79) ✓ Good H-bonds (4 bonds) ✓ Deep burial (72% SASA buried) ✓ Lipophilic contacts well-matched (84%) ✗ High strain energy (23.7 kcal/mol) ✗ Geometry warnings ✗ Many internal clashes (15)
Score
-18.845
kcal/mol
LE
-0.589
kcal/mol/HA
Fit Quality
-5.79
FQ (Leeson)
HAC
32
heavy atoms
MW
457
Da
LogP
4.90
cLogP
Strain ΔE
23.7 kcal/mol
SASA buried
72%
Lipo contact
84% BSA apolar/total
SASA unbound
733 Ų
Apolar buried
446 Ų

Interaction summary

HB 4 HY 10 PI 0 CLASH 0 ⚠ Exposure 66%
🚨Solvent-exposed hydrophobic surface — desolvation penalty likely
67% of hydrophobic surface is solvent-exposed (16/24 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 24 Buried (contacted) 8 Exposed 16 LogP 4.9 H-bonds 4
Exposed fragments: phenyl (2/5 atoms exposed)phenyl (4/6 atoms exposed)phenyl (6/6 atoms exposed)aliphatic chain/group (6 atoms exposed)
Final rank2.534Score-18.845
Inter norm-0.691Intra norm0.102
Top1000noExcludedno
Contacts13H-bonds4
Artifact reasongeometry warning; 15 clashes; 1 protein clash; moderate strain Δ 23.7
Residues
ARG22 ARG342 ASN20 ASP385 CYS26 GLN341 GLU343 GLU384 LEU25 LEU382 SER282 THR21 THR285

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

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
Jaccard0.40RMSD-
HB strict1Strict recall0.17
HB same residue+role2HB role recall0.40
HB same residue2HB residue recall0.40

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.

All stored poses for this docking hit

PoseFinal rankInter normScoreHBCTCT overlapCT recallHB role rec.RMSDExcluded
234 0.9692453899763632 -1.13913 -33.74 5 18 0 0.00 0.00 - no Open
303 1.9420000552353425 -0.811521 -24.452 3 18 0 0.00 0.00 - no Open
254 2.534061147836225 -0.691264 -18.8448 4 13 8 0.53 0.40 - no Current

Molecular metrics

RDKit SASA burial, strain energy (MMFF94s), ligand efficiency and fit quality for this docking pose.
✓ Metrics available

Scoring & efficiency
Docking score -18.845kcal/mol
Ligand efficiency (LE) -0.5889kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -5.791
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 32HA

Physicochemical properties
Molecular weight 456.6Da
Lipinski: ≤ 500 Da
LogP (cLogP) 4.90
Lipinski: ≤ 5
Rotatable bonds 7

Conformational strain (MMFF94s)
Strain energy (ΔE) 23.69kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy 110.19kcal/mol
Minimised FF energy 86.50kcal/mol

SASA & burial

✓ computed
SASA (unbound) 733.0Ų
Total solvent-accessible surface area of free ligand
BSA total 530.2Ų
Buried surface area upon binding
BSA apolar 446.3Ų
Hydrophobic contacts buried
BSA polar 83.8Ų
Polar contacts buried
Fraction buried 72.3%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 84.2%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -2596.1Ų
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 1387.1Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)