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 strong
SASA done
Strain ΔE
10.0 kcal/mol
Protein clashes
2
Internal clashes
2
Native overlap
contact recall 0.85, Jaccard 0.52
Reason: no major geometry red flags detected
2 protein-contact clashes
Molecular report
Promising
Reasonable quality metrics. Warrants further investigation.
✓ Excellent LE (-0.653 kcal/mol/HA)
✓ Good fit quality (FQ -6.37)
✓ Good H-bonds (3 bonds)
✓ Deep burial (80% SASA buried)
✓ Lipophilic contacts well-matched (99%)
✗ Moderate strain (10.0 kcal/mol)
✗ Geometry warnings
✗ Internal clashes (9)
Score
-20.253
kcal/mol
LE
-0.653
kcal/mol/HA
Fit Quality
-6.37
FQ (Leeson)
HAC
31
heavy atoms
MW
559
Da
LogP
6.72
cLogP
Interaction summary
HB 3
HY 24
PI 1
CLASH 2
Interaction summary
HB 3
HY 24
PI 1
CLASH 2
HB · H-bonds
Mode: strict. Count shows atom-level H-bonds; unique residues in summary: 0.
PI · π–π interactions
Native π–π recall is disabled because no explicit native π–π reference was stored.
HY · Hydrophobic contacts
CLASH · Clashes
| Final rank | 2.120 | Score | -20.253 |
|---|---|---|---|
| Inter norm | -0.771 | Intra norm | 0.118 |
| Top1000 | no | Excluded | no |
| Contacts | 19 | H-bonds | 3 |
| Artifact reason | geometry warning; 9 clashes; 1 protein clash | ||
| Residues |
ALA209
ALA67
ALA77
ALA90
ARG74
ASN208
GLY66
GLY85
LEU73
LYS211
LYS89
MET70
PHE83
PRO187
PRO212
PRO213
TYR210
TYR69
VAL88
| ||
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 | 11 | Native recall | 0.85 |
| Jaccard | 0.52 | 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 664 | 0.8004369919995663 | -0.933844 | -30.298 | 2 | 19 | 0 | 0.00 | - | - | no | Open |
| 675 | 0.9663918242020272 | -0.695012 | -17.6101 | 3 | 12 | 0 | 0.00 | - | - | no | Open |
| 662 | 2.0882393819561376 | -0.939599 | -24.7443 | 3 | 21 | 0 | 0.00 | - | - | no | Open |
| 670 | 2.1198155062657644 | -0.77114 | -20.2531 | 3 | 19 | 11 | 0.85 | - | - | no | Current |
Molecular metrics
RDKit SASA burial, strain energy (MMFF94s), ligand efficiency and fit quality for this docking pose.
Scoring & efficiency
Docking score
-20.253kcal/mol
Ligand efficiency (LE)
-0.6533kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-6.365
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
31HA
Physicochemical properties
Molecular weight
558.7Da
Lipinski: ≤ 500 Da
LogP (cLogP)
6.72
Lipinski: ≤ 5
Rotatable bonds
6
Conformational strain (MMFF94s)
Strain energy (ΔE)
10.04kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
60.73kcal/mol
Minimised FF energy
50.69kcal/mol
SASA & burial
✓ computed
SASA (unbound)
719.7Ų
Total solvent-accessible surface area of free ligand
BSA total
577.9Ų
Buried surface area upon binding
BSA apolar
571.3Ų
Hydrophobic contacts buried
BSA polar
6.6Ų
Polar contacts buried
Fraction buried
80.3%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
98.9%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-3173.9Ų
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
1541.1Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)