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
30.5 kcal/mol
Protein clashes
5
Internal clashes
5
Native overlap
contact recall 0.89, Jaccard 0.65, H-bond role recall 0.71
Reason: no major geometry red flags detected
5 protein-contact clashes
5 intramolecular clashes
Molecular report
Weak
Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-1.161 kcal/mol/HA)
✓ Good fit quality (FQ -10.96)
✓ Strong H-bond network (11 bonds)
✓ Deep burial (85% SASA buried)
✓ Lipophilic contacts well-matched (77%)
✗ Very high strain energy (30.5 kcal/mol)
✗ Geometry warnings
✗ Many internal clashes (12)
Score
-32.508
kcal/mol
LE
-1.161
kcal/mol/HA
Fit Quality
-10.96
FQ (Leeson)
HAC
28
heavy atoms
MW
398
Da
LogP
3.33
cLogP
Interaction summary
HB 11
HY 11
PI 3
CLASH 5
Interaction summary
HB 11
HY 11
PI 3
CLASH 5
| Final rank | 4.402 | Score | -32.508 |
|---|---|---|---|
| Inter norm | -1.302 | Intra norm | 0.141 |
| Top1000 | no | Excluded | no |
| Contacts | 24 | H-bonds | 11 |
| Artifact reason | geometry warning; 12 clashes; 2 protein clashes; high strain Δ 30.5 | ||
| Residues |
ALA111
ALA67
ARG154
ARG277
ASP233
ASP88
CYS70
GLU274
GLY199
GLY235
GLY236
GLY237
GLY276
HIS197
LYS69
PHE196
PHE238
PRO113
PRO275
SER195
SER200
THR132
TYR278
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 | 17 | Native recall | 0.89 |
| Jaccard | 0.65 | RMSD | - |
| HB strict | 7 | Strict recall | 0.78 |
| 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
| Pose | Final rank | Inter norm | Score | HB | CT | CT overlap | CT recall | HB role rec. | RMSD | Excluded | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 276 | 1.4370460415681932 | -0.857202 | -20.8428 | 4 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 279 | 1.5440426723862828 | -0.915782 | -15.5774 | 3 | 17 | 0 | 0.00 | 0.00 | - | no | Open |
| 322 | 2.2845055573682136 | -0.837043 | -14.4333 | 8 | 14 | 1 | 0.05 | 0.00 | - | no | Open |
| 328 | 3.9600681558418565 | -0.700868 | -19.9524 | 4 | 10 | 0 | 0.00 | 0.00 | - | no | Open |
| 234 | 4.402454043048613 | -1.3024 | -32.5083 | 11 | 24 | 17 | 0.89 | 0.71 | - | no | Current |
| 243 | 4.556144867088151 | -1.00584 | -21.4104 | 12 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 264 | 4.751862308706498 | -1.26026 | -34.8667 | 11 | 21 | 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
-32.508kcal/mol
Ligand efficiency (LE)
-1.1610kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-10.960
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
28HA
Physicochemical properties
Molecular weight
398.4Da
Lipinski: ≤ 500 Da
LogP (cLogP)
3.33
Lipinski: ≤ 5
Rotatable bonds
6
Conformational strain (MMFF94s)
Strain energy (ΔE)
30.54kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
-172.16kcal/mol
Minimised FF energy
-202.69kcal/mol
SASA & burial
✓ computed
SASA (unbound)
665.9Ų
Total solvent-accessible surface area of free ligand
BSA total
568.2Ų
Buried surface area upon binding
BSA apolar
437.0Ų
Hydrophobic contacts buried
BSA polar
131.2Ų
Polar contacts buried
Fraction buried
85.3%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
76.9%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-2601.5Ų
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
1386.9Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)