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
15.8 kcal/mol
Protein clashes
1
Internal clashes
1
Native overlap
contact recall 0.54, Jaccard 0.35
Reason: no major geometry red flags detected
1 protein-contact clashes
Molecular report
Promising
Reasonable quality metrics. Warrants further investigation.
✓ Excellent LE (-1.110 kcal/mol/HA)
✓ Good fit quality (FQ -9.10)
✓ Good H-bonds (5 bonds)
✓ Deep burial (84% SASA buried)
✓ Lipophilic contacts well-matched (84%)
✗ Moderate strain (15.8 kcal/mol)
✗ Geometry warnings
✗ Internal clashes (8)
Score
-21.093
kcal/mol
LE
-1.110
kcal/mol/HA
Fit Quality
-9.10
FQ (Leeson)
HAC
19
heavy atoms
MW
279
Da
LogP
2.90
cLogP
Interaction summary
HB 5
HY 24
PI 1
CLASH 1
Interaction summary
HB 5
HY 24
PI 1
CLASH 1
| Final rank | 2.149 | Score | -21.093 |
|---|---|---|---|
| Inter norm | -1.238 | Intra norm | 0.127 |
| Top1000 | no | Excluded | no |
| Contacts | 14 | H-bonds | 5 |
| Artifact reason | geometry warning; 8 clashes; 2 protein clashes | ||
| Residues |
ALA209
ALA67
ALA90
GLN68
GLY66
LEU73
LYS211
LYS89
MET70
PRO212
PRO213
TYR210
TYR69
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 | 7 | Native recall | 0.54 |
| Jaccard | 0.35 | 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
Native π–π recall is disabled because no explicit native π–π reference was stored.
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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 380 | 1.2157029303091844 | -1.31937 | -22.3757 | 8 | 12 | 0 | 0.00 | - | - | no | Open |
| 365 | 2.03476027107978 | -1.69221 | -27.2831 | 9 | 18 | 0 | 0.00 | - | - | no | Open |
| 492 | 2.149058578081181 | -1.23753 | -21.0928 | 5 | 14 | 7 | 0.54 | - | - | no | Current |
| 344 | 2.4482415740067793 | -1.45975 | -25.5076 | 10 | 13 | 0 | 0.00 | - | - | no | Open |
| 368 | 2.7696457872585443 | -1.25917 | -21.824 | 6 | 11 | 0 | 0.00 | - | - | no | Open |
| 377 | 3.074515803373726 | -1.38191 | -21.767 | 5 | 13 | 0 | 0.00 | - | - | no | Open |
| 414 | 3.32166662867758 | -1.46812 | -21.6428 | 9 | 10 | 0 | 0.00 | - | - | no | Open |
| 395 | 3.6859088691304858 | -1.28583 | -23.0255 | 8 | 14 | 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
-21.093kcal/mol
Ligand efficiency (LE)
-1.1101kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-9.100
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
19HA
Physicochemical properties
Molecular weight
278.7Da
Lipinski: ≤ 500 Da
LogP (cLogP)
2.90
Lipinski: ≤ 5
Rotatable bonds
5
Conformational strain (MMFF94s)
Strain energy (ΔE)
15.85kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
90.98kcal/mol
Minimised FF energy
75.13kcal/mol
SASA & burial
✓ computed
SASA (unbound)
486.2Ų
Total solvent-accessible surface area of free ligand
BSA total
409.5Ų
Buried surface area upon binding
BSA apolar
343.4Ų
Hydrophobic contacts buried
BSA polar
66.2Ų
Polar contacts buried
Fraction buried
84.2%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
83.8%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-2880.3Ų
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
1522.3Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)