Molecular metrics status: done
RDKit SASA-based burial metrics are cached.
SASA cached
3D complex viewer
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Protein receptor
Pocket residues
Cofactor context
Docked ligand
Overall assessment
Weak
SASA cached
Weak or marginal quality
Binding strong
Geometry medium
Native strong
SASA done
Strain ΔE
35.2 kcal/mol
Protein clashes
3
Internal clashes
3
Native overlap
contact recall 0.79, Jaccard 0.68, H-bond role recall 0.43
Reason: no major geometry red flags detected
3 protein-contact clashes
3 intramolecular clashes
48% of hydrophobic surface appears solvent-exposed (10/21 atoms). Partial exposure is common but may limit selectivity and membrane permeability.
Molecular report
Weak
Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-0.810 kcal/mol/HA)
✓ Good fit quality (FQ -7.97)
✓ Strong H-bond network (11 bonds)
✓ Deep burial (73% SASA buried)
✓ Lipophilic contacts well-matched (74%)
✗ Very high strain energy (35.2 kcal/mol)
✗ Geometry warnings
✗ Many internal clashes (10)
Score
-25.936
kcal/mol
LE
-0.810
kcal/mol/HA
Fit Quality
-7.97
FQ (Leeson)
HAC
32
heavy atoms
MW
474
Da
LogP
3.08
cLogP
Interaction summary
HB 11
HY 4
PI 4
CLASH 3
⚠ Exposure 47%
Interaction summary
HB 11
HY 4
PI 4
CLASH 3
⚠ Exposure 47%
Partial hydrophobic solvent exposure
48% of hydrophobic surface appears solvent-exposed (10/21 atoms). Partial exposure is common but may limit selectivity and membrane permeability.
Non-polar atoms 21
Buried (contacted) 11
Exposed 10
LogP 3.08
H-bonds 11
Exposed fragments:
phenyl (6/6 atoms exposed)aliphatic chain/group (4 atoms exposed)
| Final rank | 3.997 | Score | -25.936 |
|---|---|---|---|
| Inter norm | -0.873 | Intra norm | 0.062 |
| Top1000 | no | Excluded | no |
| Contacts | 18 | H-bonds | 11 |
| Artifact reason | geometry warning; 10 clashes; 2 protein clashes; high strain Δ 35.2 | ||
| Residues |
ALA111
ALA67
ARG154
ARG277
ASP332
ASP88
GLU274
GLY199
GLY236
GLY237
GLY276
HIS197
HIS333
LYS69
PHE170
SER200
TYR331
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 | 15 | Native recall | 0.79 |
| Jaccard | 0.68 | RMSD | - |
| HB strict | 4 | Strict recall | 0.44 |
| HB same residue+role | 3 | HB role recall | 0.43 |
| 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 341 | 1.1339898602829128 | -0.748485 | -23.9309 | 5 | 20 | 0 | 0.00 | 0.00 | - | no | Open |
| 303 | 1.3372398954075264 | -0.804404 | -24.1855 | 3 | 21 | 0 | 0.00 | 0.00 | - | no | Open |
| 283 | 2.139474337523808 | -0.817859 | -25.2468 | 5 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 371 | 2.559480306330345 | -0.816062 | -23.2325 | 7 | 17 | 0 | 0.00 | 0.00 | - | no | Open |
| 354 | 2.6386474714478307 | -0.812846 | -23.9788 | 3 | 17 | 0 | 0.00 | 0.00 | - | no | Open |
| 301 | 2.8439180620978584 | -0.787716 | -20.8602 | 8 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 321 | 2.895404379539044 | -0.670765 | -19.5853 | 8 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 275 | 3.0839455449061752 | -0.895097 | -27.2356 | 6 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 263 | 3.997061431046954 | -0.87282 | -25.9359 | 11 | 18 | 15 | 0.79 | 0.43 | - | no | Current |
| 323 | 5.661054598843183 | -0.800961 | -21.9554 | 9 | 18 | 0 | 0.00 | 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
-25.936kcal/mol
Ligand efficiency (LE)
-0.8105kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-7.970
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
32HA
Physicochemical properties
Molecular weight
473.6Da
Lipinski: ≤ 500 Da
LogP (cLogP)
3.08
Lipinski: ≤ 5
Rotatable bonds
9
Conformational strain (MMFF94s)
Strain energy (ΔE)
35.24kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
-68.68kcal/mol
Minimised FF energy
-103.92kcal/mol
SASA & burial
✓ computed
SASA (unbound)
728.5Ų
Total solvent-accessible surface area of free ligand
BSA total
532.5Ų
Buried surface area upon binding
BSA apolar
392.9Ų
Hydrophobic contacts buried
BSA polar
139.7Ų
Polar contacts buried
Fraction buried
73.1%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
73.8%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-2593.8Ų
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
1410.0Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)