Molecular metrics status: done
RDKit SASA-based burial metrics are cached.
SASA cached
3D complex viewer
Viewer legend
Protein receptor
Pocket residues
Cofactor context
Docked ligand
Overall assessment
Promising
SASA cached
Promising and worth follow-up
Binding strong
Geometry high
Native mixed
SASA done
Strain ΔE
15.3 kcal/mol
Protein clashes
1
Internal clashes
1
Native overlap
contact recall 0.46, Jaccard 0.32
Reason: no major geometry red flags detected
1 protein-contact clashes
Molecular report
Promising
Reasonable quality metrics. Warrants further investigation.
✓ Excellent LE (-1.308 kcal/mol/HA)
✓ Good fit quality (FQ -10.72)
✓ Strong H-bond network (7 bonds)
✓ Deep burial (70% SASA buried)
✓ Lipophilic contacts well-matched (82%)
✗ Moderate strain (15.3 kcal/mol)
✗ Geometry warnings
✗ Internal clashes (6)
Score
-24.846
kcal/mol
LE
-1.308
kcal/mol/HA
Fit Quality
-10.72
FQ (Leeson)
HAC
19
heavy atoms
MW
263
Da
LogP
0.28
cLogP
Interaction summary
HB 7
HY 12
PI 0
CLASH 1
Interaction summary
HB 7
HY 12
PI 0
CLASH 1
| Final rank | 3.340 | Score | -24.846 |
|---|---|---|---|
| Inter norm | -1.451 | Intra norm | 0.143 |
| Top1000 | no | Excluded | no |
| Contacts | 12 | H-bonds | 7 |
| Artifact reason | geometry warning; 6 clashes; 3 protein clashes | ||
| Residues |
ALA90
ASN91
GLY214
GLY215
LYS211
LYS89
PRO187
PRO212
PRO213
TRP92
TYR210
VAL88
| ||
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 | ||
Native ligand reference
★ reference
Interaction fingerprint calculated directly from the uploaded native ligand without docking. Current H-bond mode: strict.
| 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 | 6 | Native recall | 0.46 |
| Jaccard | 0.32 | RMSD | - |
| HB strict | 0 | Strict recall | - |
| HB same residue+role | 0 | HB role recall | - |
| HB same residue | 0 | HB residue recall | - |
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
All stored poses for this docking hit
| Pose | Final rank | Inter norm | Score | HB | CT | CT overlap | CT recall | HB role rec. | RMSD | Excluded | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 269 | 1.9744945659750004 | -1.07862 | -18.0223 | 6 | 9 | 0 | 0.00 | - | - | no | Open |
| 238 | 2.100724177218206 | -1.53049 | -25.0062 | 5 | 10 | 0 | 0.00 | - | - | no | Open |
| 225 | 3.2749514114110547 | -1.60122 | -28.4044 | 8 | 16 | 0 | 0.00 | - | - | no | Open |
| 354 | 3.339664030123585 | -1.4508 | -24.8462 | 7 | 12 | 6 | 0.46 | - | - | no | Current |
Molecular metrics
RDKit SASA burial, strain energy (MMFF94s), ligand efficiency and fit quality for this docking pose.
Scoring & efficiency
Docking score
-24.846kcal/mol
Ligand efficiency (LE)
-1.3077kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-10.719
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
19HA
Physicochemical properties
Molecular weight
263.3Da
Lipinski: ≤ 500 Da
LogP (cLogP)
0.28
Lipinski: ≤ 5
Rotatable bonds
7
Conformational strain (MMFF94s)
Strain energy (ΔE)
15.33kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
34.23kcal/mol
Minimised FF energy
18.89kcal/mol
SASA & burial
✓ computed
SASA (unbound)
527.8Ų
Total solvent-accessible surface area of free ligand
BSA total
367.5Ų
Buried surface area upon binding
BSA apolar
299.9Ų
Hydrophobic contacts buried
BSA polar
67.6Ų
Polar contacts buried
Fraction buried
69.6%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
81.6%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-2927.2Ų
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
1537.7Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)