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 strong
SASA done
Strain ΔE
14.4 kcal/mol
Protein clashes
3
Internal clashes
3
Native overlap
contact recall 0.74, Jaccard 0.61, H-bond role recall 0.57
Reason: no major geometry red flags detected
3 protein-contact clashes
3 intramolecular clashes
Molecular report
Promising
Reasonable quality metrics. Warrants further investigation.
✓ Excellent LE (-0.959 kcal/mol/HA)
✓ Good fit quality (FQ -8.95)
✓ Strong H-bond network (8 bonds)
✓ Deep burial (73% SASA buried)
✓ Lipophilic contacts well-matched (68%)
✗ Moderate strain (14.4 kcal/mol)
✗ Geometry warnings
✗ Internal clashes (9)
Score
-25.898
kcal/mol
LE
-0.959
kcal/mol/HA
Fit Quality
-8.95
FQ (Leeson)
HAC
27
heavy atoms
MW
402
Da
LogP
2.26
cLogP
Interaction summary
HB 8
HY 11
PI 3
CLASH 3
Interaction summary
HB 8
HY 11
PI 3
CLASH 3
| Final rank | 4.314 | Score | -25.898 |
|---|---|---|---|
| Inter norm | -1.019 | Intra norm | 0.060 |
| Top1000 | no | Excluded | no |
| Contacts | 18 | H-bonds | 8 |
| Artifact reason | geometry warning; 9 clashes; 3 protein clashes | ||
| Residues |
ALA67
ARG277
ASN327
ASP332
GLU274
GLY199
GLY236
GLY237
GLY276
GLY393
HIS197
LYS69
PHE238
PRO275
SER200
TYR331
TYR389
VAL392
| ||
Protein summary
411 residues
| Protein target | T13 | Atoms | 6340 |
|---|---|---|---|
| Residues | 411 | Chains | 1 |
| Residue summary | VAL:624; LEU:551; LYS:506; ARG:480; PHE:460; ILE:418; ASP:348; GLU:332; THR:322; TYR:315; PRO:308; ALA:290; SER:264; GLY:224; ASN:210; GLN:170 | ||
Native ligand reference
★ reference
Interaction fingerprint calculated directly from the uploaded native ligand without docking. Current H-bond mode: strict.
| Name | 1F3T | Contacts | 19 |
|---|---|---|---|
| Pose | Open native pose | HB | 0 |
| IFP residues |
ALA111
ALA67
ARG154
ARG277
ASP332
ASP88
CYS70
GLU274
GLY236
GLY237
GLY276
HIS197
LYS69
PHE238
PRO275
SER200
TYR278
TYR331
TYR389
| ||
| Current overlap | 14 | Native recall | 0.74 |
| Jaccard | 0.61 | RMSD | - |
| HB strict | 5 | Strict recall | 0.56 |
| HB same residue+role | 4 | HB role recall | 0.57 |
| HB same residue | 4 | HB residue recall | 0.57 |
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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 413 | 4.313562737032811 | -1.0187 | -25.8976 | 8 | 18 | 14 | 0.74 | 0.57 | - | no | Current |
Molecular metrics
RDKit SASA burial, strain energy (MMFF94s), ligand efficiency and fit quality for this docking pose.
Scoring & efficiency
Docking score
-25.898kcal/mol
Ligand efficiency (LE)
-0.9592kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-8.949
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
27HA
Physicochemical properties
Molecular weight
401.5Da
Lipinski: ≤ 500 Da
LogP (cLogP)
2.26
Lipinski: ≤ 5
Rotatable bonds
3
Conformational strain (MMFF94s)
Strain energy (ΔE)
14.41kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
1.05kcal/mol
Minimised FF energy
-13.36kcal/mol
SASA & burial
✓ computed
SASA (unbound)
634.7Ų
Total solvent-accessible surface area of free ligand
BSA total
463.9Ų
Buried surface area upon binding
BSA apolar
313.5Ų
Hydrophobic contacts buried
BSA polar
150.4Ų
Polar contacts buried
Fraction buried
73.1%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
67.6%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-2541.5Ų
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
3461.2Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA
1373.3Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)