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 medium
Native mixed
SASA done
Strain ΔE
13.1 kcal/mol
Protein clashes
4
Internal clashes
4
Native overlap
contact recall 0.46, Jaccard 0.33
Reason: no major geometry red flags detected
4 protein-contact clashes
4 intramolecular clashes
Molecular report
Promising
Reasonable quality metrics. Warrants further investigation.
✓ Excellent LE (-1.000 kcal/mol/HA)
✓ Good fit quality (FQ -8.53)
✓ Strong H-bond network (6 bonds)
✓ Deep burial (68% SASA buried)
✓ Lipophilic contacts well-matched (76%)
✗ Moderate strain (13.1 kcal/mol)
✗ Geometry warnings
✗ Internal clashes (9)
Score
-21.000
kcal/mol
LE
-1.000
kcal/mol/HA
Fit Quality
-8.53
FQ (Leeson)
HAC
21
heavy atoms
MW
306
Da
LogP
2.73
cLogP
Interaction summary
HB 6
HY 24
PI 0
CLASH 4
Interaction summary
HB 6
HY 24
PI 0
CLASH 4
| Final rank | 3.929 | Score | -21.000 |
|---|---|---|---|
| Inter norm | -1.149 | Intra norm | 0.149 |
| Top1000 | no | Excluded | no |
| Contacts | 11 | H-bonds | 6 |
| Artifact reason | geometry warning; 9 clashes; 3 protein clashes | ||
| Residues |
ALA90
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 | 0.33 | 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 407 | 2.7701591179867786 | -1.0811 | -20.1761 | 6 | 10 | 0 | 0.00 | - | - | no | Open |
| 503 | 3.928925091213071 | -1.1487 | -21.0002 | 6 | 11 | 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
-21.000kcal/mol
Ligand efficiency (LE)
-1.0000kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-8.530
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
21HA
Physicochemical properties
Molecular weight
305.8Da
Lipinski: ≤ 500 Da
LogP (cLogP)
2.73
Lipinski: ≤ 5
Rotatable bonds
4
Conformational strain (MMFF94s)
Strain energy (ΔE)
13.12kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
99.29kcal/mol
Minimised FF energy
86.17kcal/mol
SASA & burial
✓ computed
SASA (unbound)
507.3Ų
Total solvent-accessible surface area of free ligand
BSA total
346.4Ų
Buried surface area upon binding
BSA apolar
264.9Ų
Hydrophobic contacts buried
BSA polar
81.5Ų
Polar contacts buried
Fraction buried
68.3%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
76.5%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-2859.4Ų
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
1560.2Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)