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 medium
Native strong
SASA done
Strain ΔE
19.9 kcal/mol
Protein clashes
4
Internal clashes
4
Native overlap
contact recall 0.79, Jaccard 0.60, H-bond role recall 0.29
Reason: no major geometry red flags detected
4 protein-contact clashes
4 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 High
Ames Clear
DILI Risk
Molecular report
Promising
Reasonable quality metrics. Warrants further investigation.
✓ Excellent LE (-0.819 kcal/mol/HA)
✓ Good fit quality (FQ -7.90)
✓ Good H-bonds (5 bonds)
✓ Deep burial (78% SASA buried)
✓ Lipophilic contacts well-matched (66%)
✗ Moderate strain (19.9 kcal/mol)
✗ Geometry warnings
✗ Internal clashes (6)
Score
-24.569
kcal/mol
LE
-0.819
kcal/mol/HA
Fit Quality
-7.90
FQ (Leeson)
HAC
30
heavy atoms
MW
458
Da
LogP
4.39
cLogP
Final rank
2.3929
rank score
Inter norm
-0.946
normalised
Contacts
21
H-bonds 8
Interaction summary
HBD 2
HBA 3
PC 1
HY 5
PI 3
CLASH 4
Interaction summary
HBD 2
HBA 3
PC 1
HY 5
PI 3
CLASH 4
HBD/HBA · H-bonds (geometric)
HBD = ligand donates H · HBA = ligand accepts H · ~ = weak (≥110°). Mode: strict. Residues: 5.
PC · Polar contacts (possible, no H geometry)
HBD?/HBA? — heavy-atom distance only, H geometry unavailable. May be real H-bonds.
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 | 15 | Native recall | 0.79 |
| Jaccard | 0.60 | RMSD | - |
| HB strict | 2 | Strict recall | 0.22 |
| HB same residue+role | 2 | HB role recall | 0.29 |
| HB same residue | 2 | HB residue recall | 0.29 |
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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 628 | 0.008854525213062667 | -1.14295 | -33.0619 | 7 | 13 | 0 | 0.00 | 0.00 | - | no | Open |
| 627 | 1.1396758497593025 | -1.05588 | -30.4855 | 5 | 17 | 0 | 0.00 | 0.00 | - | no | Open |
| 634 | 1.7982601596722638 | -0.977273 | -27.7572 | 6 | 11 | 0 | 0.00 | 0.00 | - | no | Open |
| 646 | 2.3929112179154344 | -0.946387 | -24.5689 | 8 | 21 | 15 | 0.79 | 0.29 | - | no | Current |
| 647 | 3.175551530334193 | -1.01731 | -26.2245 | 7 | 14 | 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
-24.569kcal/mol
Ligand efficiency (LE)
-0.8190kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-7.900
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
30HA
Physicochemical properties
Molecular weight
457.6Da
Lipinski: ≤ 500 Da
LogP (cLogP)
4.39
Lipinski: ≤ 5
Rotatable bonds
7
Conformational strain (MMFF94s)
Strain energy (ΔE)
19.95kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
-16.47kcal/mol
Minimised FF energy
-36.41kcal/mol
SASA & burial
✓ computed
SASA (unbound)
725.4Ų
Total solvent-accessible surface area of free ligand
BSA total
569.7Ų
Buried surface area upon binding
BSA apolar
378.6Ų
Hydrophobic contacts buried
BSA polar
191.1Ų
Polar contacts buried
Fraction buried
78.5%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
66.5%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-2589.6Ų
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
1387.5Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)