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
22.5 kcal/mol
Protein clashes
4
Internal clashes
4
Native overlap
contact recall 0.74, Jaccard 0.67, H-bond role recall 0.57
Reason: no major geometry red flags detected
4 protein-contact clashes
4 intramolecular 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
Weak
Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-1.254 kcal/mol/HA)
✓ Good fit quality (FQ -10.27)
✓ Good H-bonds (5 bonds)
✓ Deep burial (75% SASA buried)
✓ Lipophilic contacts well-matched (74%)
✗ High strain energy (22.5 kcal/mol)
✗ Geometry warnings
✗ Internal clashes (9)
Score
-23.816
kcal/mol
LE
-1.254
kcal/mol/HA
Fit Quality
-10.27
FQ (Leeson)
HAC
19
heavy atoms
MW
254
Da
LogP
2.41
cLogP
Final rank
3.8864
rank score
Inter norm
-1.455
normalised
Contacts
16
H-bonds 7
Interaction summary
HBD 1
HBA 4
HY 0
PI 3
CLASH 4
Interaction summary
HBD 1
HBA 4
HY 0
PI 3
CLASH 4
HBD/HBA · H-bonds (geometric)
HBD = ligand donates H · HBA = ligand accepts H · ~ = weak (≥110°). Mode: strict. Residues: 5.
PI · π–π interactions
Native π–π recall is disabled because no explicit native π–π reference was stored.
HY · Hydrophobic contacts
No hy · hydrophobic contacts detected for this pose.
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 | 14 | Native recall | 0.74 |
| Jaccard | 0.67 | RMSD | - |
| HB strict | 4 | Strict recall | 0.44 |
| 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 599 | 1.774607054232465 | -1.34971 | -23.3525 | 7 | 13 | 0 | 0.00 | 0.00 | - | no | Open |
| 626 | 2.9890510231618737 | -1.2951 | -22.6337 | 10 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 609 | 3.0159037591829456 | -1.44252 | -25.0979 | 8 | 12 | 0 | 0.00 | 0.00 | - | no | Open |
| 624 | 3.0872971814603587 | -1.32537 | -23.3887 | 7 | 13 | 0 | 0.00 | 0.00 | - | no | Open |
| 618 | 3.1835171244642915 | -1.27025 | -21.0326 | 7 | 13 | 0 | 0.00 | 0.00 | - | no | Open |
| 600 | 3.7608836455983226 | -1.51756 | -26.9668 | 8 | 14 | 0 | 0.00 | 0.00 | - | no | Open |
| 620 | 3.8864306304714464 | -1.45494 | -23.8158 | 7 | 16 | 14 | 0.74 | 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
-23.816kcal/mol
Ligand efficiency (LE)
-1.2535kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-10.274
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
19HA
Physicochemical properties
Molecular weight
254.2Da
Lipinski: ≤ 500 Da
LogP (cLogP)
2.41
Lipinski: ≤ 5
Rotatable bonds
3
Conformational strain (MMFF94s)
Strain energy (ΔE)
22.49kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
25.76kcal/mol
Minimised FF energy
3.27kcal/mol
SASA & burial
✓ computed
SASA (unbound)
464.6Ų
Total solvent-accessible surface area of free ligand
BSA total
349.4Ų
Buried surface area upon binding
BSA apolar
256.8Ų
Hydrophobic contacts buried
BSA polar
92.7Ų
Polar contacts buried
Fraction buried
75.2%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
73.5%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-2412.6Ų
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
1404.4Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)