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 but geometrically suspicious
Binding strong
Geometry low
Native strong
SASA done
Strain ΔE
15.6 kcal/mol
Protein clashes
0
Internal clashes
8
Native overlap
contact recall 0.74, Jaccard 0.58, H-bond role recall 0.57
Reason: 8 internal clashes
8 intramolecular clashes
EcoTox / ADMET
In-silico prediction only
Fish LC₅₀
Cat. 2 — Toxic (1–10 mg/L)
Daphnia EC₅₀
Cat. 2 — Toxic (1–10 mg/L)
Algae IC₅₀
Cat. 2 — Toxic (1–10 mg/L)
Bioaccum.
Not B (BCF≤2000)
Persistent
No
ADMET alerts (in-silico)
hERG Low
Ames Clear
DILI Low
Molecular report
Promising
Reasonable quality metrics. Warrants further investigation.
✓ Excellent LE (-0.927 kcal/mol/HA)
✓ Good fit quality (FQ -8.75)
✓ Strong H-bond network (7 bonds)
✓ Deep burial (81% SASA buried)
✓ Lipophilic contacts well-matched (74%)
✗ Moderate strain (15.6 kcal/mol)
✗ Geometry warnings
✗ Internal clashes (8)
Score
-25.964
kcal/mol
LE
-0.927
kcal/mol/HA
Fit Quality
-8.75
FQ (Leeson)
HAC
28
heavy atoms
MW
413
Da
LogP
3.65
cLogP
Final rank
3.3289
rank score
Inter norm
-1.031
normalised
Contacts
19
H-bonds 9
Interaction summary
HBA 7
HY 4
PI 3
CLASH 0
Interaction summary
HBA 7
HY 4
PI 3
CLASH 0
HBD/HBA · H-bonds (geometric)
HBD = ligand donates H · HBA = ligand accepts H · ~ = weak (≥110°). Mode: strict. Residues: 3.
PI · π–π interactions
Native π–π recall is disabled because no explicit native π–π reference was stored.
HY · Hydrophobic contacts
CLASH · Clashes
No clash · clashes detected for this pose.
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 | 0.58 | 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 |
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 | ||
All stored poses for this docking hit
| Pose | Final rank | Inter norm | Score | HB | CT | CT overlap | CT recall | HB role rec. | RMSD | Excluded | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 663 | 0.2511577254753023 | -1.09851 | -30.8922 | 4 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 646 | 0.8020123366541132 | -0.883354 | -23.985 | 2 | 18 | 0 | 0.00 | 0.00 | - | no | Open |
| 644 | 2.060226456342705 | -0.948105 | -29.2566 | 6 | 11 | 0 | 0.00 | 0.00 | - | no | Open |
| 673 | 2.3297314190059755 | -1.12086 | -24.7821 | 13 | 14 | 0 | 0.00 | 0.00 | - | no | Open |
| 671 | 2.7084623141150126 | -0.874177 | -26.6575 | 13 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 643 | 3.017585003862393 | -0.904163 | -23.0924 | 5 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 668 | 3.3289291970169095 | -1.03104 | -25.9639 | 9 | 19 | 14 | 0.74 | 0.57 | - | no | Current |
| 639 | 3.377817040032817 | -0.950565 | -28.199 | 7 | 13 | 0 | 0.00 | 0.00 | - | no | Open |
| 662 | 3.4574628969651684 | -0.923998 | -27.0934 | 13 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 655 | 5.144145577855445 | -1.05202 | -28.4978 | 16 | 20 | 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
-25.964kcal/mol
Ligand efficiency (LE)
-0.9273kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-8.754
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
28HA
Physicochemical properties
Molecular weight
412.9Da
Lipinski: ≤ 500 Da
LogP (cLogP)
3.65
Lipinski: ≤ 5
Rotatable bonds
6
Conformational strain (MMFF94s)
Strain energy (ΔE)
15.61kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
93.42kcal/mol
Minimised FF energy
77.80kcal/mol
SASA & burial
✓ computed
SASA (unbound)
667.8Ų
Total solvent-accessible surface area of free ligand
BSA total
539.2Ų
Buried surface area upon binding
BSA apolar
401.5Ų
Hydrophobic contacts buried
BSA polar
137.7Ų
Polar contacts buried
Fraction buried
80.7%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
74.5%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-2547.9Ų
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
1386.4Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)