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
14.3 kcal/mol
Protein clashes
2
Internal clashes
2
Native overlap
contact recall 0.63, Jaccard 0.57, H-bond role recall 0.57
Reason: no major geometry red flags detected
2 protein-contact clashes
EcoTox / ADMET
In-silico prediction only
Fish LC₅₀
Cat. 3 — Harmful (10–100 mg/L)
Daphnia EC₅₀
Cat. 3 — Harmful (10–100 mg/L)
Algae IC₅₀
Cat. 3 — Harmful (10–100 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 (-1.364 kcal/mol/HA)
✓ Good fit quality (FQ -11.63)
✓ Strong H-bond network (9 bonds)
✓ Deep burial (78% SASA buried)
✓ Lipophilic contacts well-matched (62%)
✗ Moderate strain (14.3 kcal/mol)
✗ Geometry warnings
✗ Internal clashes (5)
Score
-28.641
kcal/mol
LE
-1.364
kcal/mol/HA
Fit Quality
-11.63
FQ (Leeson)
HAC
21
heavy atoms
MW
336
Da
LogP
3.17
cLogP
Final rank
4.0800
rank score
Inter norm
-1.435
normalised
Contacts
14
H-bonds 11
Interaction summary
HBA 9
HY 2
PI 3
CLASH 2
Interaction summary
HBA 9
HY 2
PI 3
CLASH 2
HBD/HBA · H-bonds (geometric)
HBD = ligand donates H · HBA = ligand accepts H · ~ = weak (≥110°). Mode: strict. Residues: 4.
PI · π–π interactions
Native π–π recall is disabled because no explicit native π–π reference was stored.
HY · Hydrophobic contacts
CLASH · Clashes
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 | 12 | Native recall | 0.63 |
| Jaccard | 0.57 | 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
Molecular metrics
RDKit SASA burial, strain energy (MMFF94s), ligand efficiency and fit quality for this docking pose.
Scoring & efficiency
Docking score
-28.641kcal/mol
Ligand efficiency (LE)
-1.3639kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-11.633
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
21HA
Physicochemical properties
Molecular weight
336.5Da
Lipinski: ≤ 500 Da
LogP (cLogP)
3.17
Lipinski: ≤ 5
Rotatable bonds
6
Conformational strain (MMFF94s)
Strain energy (ΔE)
14.30kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
29.81kcal/mol
Minimised FF energy
15.51kcal/mol
SASA & burial
✓ computed
SASA (unbound)
553.2Ų
Total solvent-accessible surface area of free ligand
BSA total
430.4Ų
Buried surface area upon binding
BSA apolar
268.5Ų
Hydrophobic contacts buried
BSA polar
161.8Ų
Polar contacts buried
Fraction buried
77.8%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
62.4%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-2409.1Ų
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
1383.0Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)