Molecular metrics status: done
RDKit SASA-based burial metrics are cached.
SASA cached
3D complex viewer
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Protein receptor
Pocket residues
Cofactor context
Docked ligand
Overall assessment
Promising
SASA cached
Promising and worth follow-up
Binding strong
Geometry medium
Native strong
SASA done
Strain ΔE
14.1 kcal/mol
Protein clashes
3
Internal clashes
3
Native overlap
contact recall 0.77, Jaccard 0.56
Reason: no major geometry red flags detected
3 protein-contact clashes
3 intramolecular clashes
61% of hydrophobic surface is solvent-exposed (11/18 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
Promising
Reasonable quality metrics. Warrants further investigation.
✓ Excellent LE (-0.990 kcal/mol/HA)
✓ Good fit quality (FQ -9.12)
✓ Good H-bonds (3 bonds)
✓ Deep burial (66% SASA buried)
✓ Lipophilic contacts well-matched (79%)
✗ Moderate strain (14.1 kcal/mol)
✗ Geometry warnings
✗ Internal clashes (9)
Score
-25.749
kcal/mol
LE
-0.990
kcal/mol/HA
Fit Quality
-9.12
FQ (Leeson)
HAC
26
heavy atoms
MW
394
Da
LogP
2.21
cLogP
Final rank
2.0926
rank score
Inter norm
-1.013
normalised
Contacts
15
H-bonds 4
Interaction summary
HBD 1
HBA 2
HY 9
PI 1
CLASH 3
Interaction summary
HBD 1
HBA 2
HY 9
PI 1
CLASH 3
HBD/HBA · H-bonds (geometric)
HBD = ligand donates H · HBA = ligand accepts H · ~ = weak (≥110°). Mode: permissive. Residues: 3.
PI · π–π interactions
Native π–π recall is disabled because no explicit native π–π reference was stored.
HY · Hydrophobic contacts
CLASH · Clashes
Native ligand reference
★ reference
Interaction fingerprint calculated directly from the uploaded native ligand without docking. Current H-bond mode: permissive.
| Name | 9IFF | Contacts | 13 |
|---|---|---|---|
| Pose | Open native pose | HB | 0 |
| IFP residues |
ALA209
ARG74
ASN208
GLY214
GLY215
GLY85
LEU73
LYS211
MET70
PHE83
PRO212
PRO213
VAL88
| ||
| Current overlap | 10 | Native recall | 0.77 |
| Jaccard | 0.56 | RMSD | - |
| HB strict | 0 | Strict recall | - |
| HB same residue+role | 0 | HB role recall | - |
| HB same residue | 0 | HB residue recall | - |
Protein summary
489 residues
| Protein target | T15 | Atoms | 7420 |
|---|---|---|---|
| Residues | 489 | Chains | 1 |
| Residue summary | VAL: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:204 | ||
All stored poses for this docking hit
| Pose | Final rank | Inter norm | Score | HB | CT | CT overlap | CT recall | HB role rec. | RMSD | Excluded | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 556 | 2.0926180314064013 | -1.01266 | -25.749 | 4 | 15 | 10 | 0.77 | - | - | no | Current |
| 507 | 3.18817874933248 | -1.212 | -29.9184 | 7 | 22 | 0 | 0.00 | - | - | no | Open |
Molecular metrics
RDKit SASA burial, strain energy (MMFF94s), ligand efficiency and fit quality for this docking pose.
Scoring & efficiency
Docking score
-25.749kcal/mol
Ligand efficiency (LE)
-0.9903kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-9.124
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
26HA
Physicochemical properties
Molecular weight
393.5Da
Lipinski: ≤ 500 Da
LogP (cLogP)
2.21
Lipinski: ≤ 5
Rotatable bonds
4
Conformational strain (MMFF94s)
Strain energy (ΔE)
14.09kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
-43.93kcal/mol
Minimised FF energy
-58.02kcal/mol
SASA & burial
✓ computed
SASA (unbound)
640.0Ų
Total solvent-accessible surface area of free ligand
BSA total
422.6Ų
Buried surface area upon binding
BSA apolar
333.8Ų
Hydrophobic contacts buried
BSA polar
88.8Ų
Polar contacts buried
Fraction buried
66.0%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
79.0%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-2949.2Ų
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
4005.2Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA
1570.6Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)