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
15.5 kcal/mol
Protein clashes
2
Internal clashes
2
Native overlap
contact recall 0.68, Jaccard 0.62, H-bond role recall 0.71
Reason: no major geometry red flags detected
2 protein-contact clashes
Molecular report
Promising
Reasonable quality metrics. Warrants further investigation.
✓ Excellent LE (-1.219 kcal/mol/HA)
✓ Good fit quality (FQ -10.76)
✓ Strong H-bond network (12 bonds)
✓ Deep burial (74% SASA buried)
✓ Lipophilic contacts well-matched (64%)
✗ Moderate strain (15.5 kcal/mol)
✗ Geometry warnings
✗ Internal clashes (7)
Score
-28.028
kcal/mol
LE
-1.219
kcal/mol/HA
Fit Quality
-10.76
FQ (Leeson)
HAC
23
heavy atoms
MW
328
Da
LogP
2.78
cLogP
Interaction summary
HB 12
HY 3
PI 2
CLASH 2
Interaction summary
HB 12
HY 3
PI 2
CLASH 2
| Final rank | 2.775 | Score | -28.028 |
|---|---|---|---|
| Inter norm | -1.302 | Intra norm | 0.082 |
| Top1000 | no | Excluded | no |
| Contacts | 15 | H-bonds | 12 |
| Artifact reason | geometry warning; 7 clashes; 2 protein clashes | ||
| Residues |
ALA67
ARG277
ASP332
ASP88
GLU274
GLY199
GLY236
GLY237
GLY276
HIS197
HIS333
LYS69
PRO275
SER200
TYR389
| ||
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 | 13 | Native recall | 0.68 |
| Jaccard | 0.62 | RMSD | - |
| HB strict | 6 | Strict recall | 0.67 |
| HB same residue+role | 5 | HB role recall | 0.71 |
| HB same residue | 5 | HB residue recall | 0.71 |
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
Molecular metrics
RDKit SASA burial, strain energy (MMFF94s), ligand efficiency and fit quality for this docking pose.
Scoring & efficiency
Docking score
-28.028kcal/mol
Ligand efficiency (LE)
-1.2186kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-10.755
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
23HA
Physicochemical properties
Molecular weight
328.4Da
Lipinski: ≤ 500 Da
LogP (cLogP)
2.78
Lipinski: ≤ 5
Rotatable bonds
6
Conformational strain (MMFF94s)
Strain energy (ΔE)
15.47kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
100.72kcal/mol
Minimised FF energy
85.25kcal/mol
SASA & burial
✓ computed
SASA (unbound)
559.8Ų
Total solvent-accessible surface area of free ligand
BSA total
415.1Ų
Buried surface area upon binding
BSA apolar
267.0Ų
Hydrophobic contacts buried
BSA polar
148.0Ų
Polar contacts buried
Fraction buried
74.1%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
64.3%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-2456.7Ų
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
1389.9Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)