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
37.2 kcal/mol
Protein clashes
4
Internal clashes
4
Native overlap
contact recall 0.84, Jaccard 0.59, H-bond role recall 0.57
Reason: no major geometry red flags detected
4 protein-contact clashes
4 intramolecular clashes
Molecular report
Weak
Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-0.864 kcal/mol/HA)
✓ Good fit quality (FQ -8.41)
✓ Strong H-bond network (13 bonds)
✓ Deep burial (84% SASA buried)
✓ Lipophilic contacts well-matched (84%)
✗ Very high strain energy (37.2 kcal/mol)
✗ Geometry warnings
✗ Many internal clashes (15)
Score
-26.777
kcal/mol
LE
-0.864
kcal/mol/HA
Fit Quality
-8.41
FQ (Leeson)
HAC
31
heavy atoms
MW
436
Da
LogP
4.28
cLogP
Interaction summary
HB 13
HY 5
PI 3
CLASH 4
Interaction summary
HB 13
HY 5
PI 3
CLASH 4
| Final rank | 6.101 | Score | -26.777 |
|---|---|---|---|
| Inter norm | -0.998 | Intra norm | 0.134 |
| Top1000 | no | Excluded | no |
| Contacts | 24 | H-bonds | 13 |
| Artifact reason | geometry warning; 15 clashes; 4 protein clashes; high strain Δ 37.2 | ||
| Residues |
ALA111
ALA67
ARG154
ARG277
ASP233
ASP332
ASP88
GLU274
GLY199
GLY235
GLY236
GLY237
GLY276
HIS197
HIS333
LYS69
PHE196
PRO113
PRO275
SER195
SER200
THR132
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 | 16 | Native recall | 0.84 |
| Jaccard | 0.59 | 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 439 | 1.9713892149489507 | -0.828513 | -23.0655 | 4 | 17 | 0 | 0.00 | 0.00 | - | no | Open |
| 331 | 6.101128195026116 | -0.998232 | -26.7772 | 13 | 24 | 16 | 0.84 | 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
-26.777kcal/mol
Ligand efficiency (LE)
-0.8638kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-8.415
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
31HA
Physicochemical properties
Molecular weight
435.9Da
Lipinski: ≤ 500 Da
LogP (cLogP)
4.28
Lipinski: ≤ 5
Rotatable bonds
7
Conformational strain (MMFF94s)
Strain energy (ΔE)
37.17kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
122.47kcal/mol
Minimised FF energy
85.30kcal/mol
SASA & burial
✓ computed
SASA (unbound)
714.6Ų
Total solvent-accessible surface area of free ligand
BSA total
603.4Ų
Buried surface area upon binding
BSA apolar
509.1Ų
Hydrophobic contacts buried
BSA polar
94.3Ų
Polar contacts buried
Fraction buried
84.4%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
84.4%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-2644.8Ų
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
1429.5Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)