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
39.7 kcal/mol
Protein clashes
2
Internal clashes
2
Native overlap
contact recall 0.68, Jaccard 0.57, H-bond role recall 0.43
Reason: no major geometry red flags detected
2 protein-contact clashes
43% of hydrophobic surface appears solvent-exposed (13/30 atoms). Partial exposure is common but may limit selectivity and membrane permeability.
EcoTox / ADMET
In-silico prediction only
Fish LC₅₀
Cat. 1 — Very toxic (≤1 mg/L)
Daphnia EC₅₀
Cat. 1 — Very toxic (≤1 mg/L)
Algae IC₅₀
Cat. 1 — Very toxic (≤1 mg/L)
Bioaccum.
Not B (BCF≤2000)
Persistent
Yes
ADMET alerts (in-silico)
hERG High
Ames Clear
DILI Risk
Molecular report
Weak
Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-0.692 kcal/mol/HA)
✓ Good fit quality (FQ -7.13)
✓ Strong H-bond network (6 bonds)
✓ Deep burial (73% SASA buried)
✓ Lipophilic contacts well-matched (83%)
✗ Very high strain energy (39.7 kcal/mol)
✗ Geometry warnings
✗ Many internal clashes (16)
Score
-26.286
kcal/mol
LE
-0.692
kcal/mol/HA
Fit Quality
-7.13
FQ (Leeson)
HAC
38
heavy atoms
MW
515
Da
LogP
5.18
cLogP
Final rank
3.1723
rank score
Inter norm
-0.737
normalised
Contacts
17
H-bonds 7
Interaction summary
HBA 6
HY 3
PI 3
CLASH 2
Interaction summary
HBA 6
HY 3
PI 3
CLASH 2
HBD/HBA · H-bonds (geometric)
HBD = ligand donates H · HBA = ligand accepts H · ~ = weak (≥110°). Mode: strict. Residues: 2.
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 | 13 | Native recall | 0.68 |
| Jaccard | 0.57 | RMSD | - |
| HB strict | 4 | Strict recall | 0.44 |
| HB same residue+role | 3 | HB role recall | 0.43 |
| HB same residue | 3 | HB residue recall | 0.43 |
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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 170 | 3.1723182648743555 | -0.737232 | -26.286 | 7 | 17 | 13 | 0.68 | 0.43 | - | no | Current |
| 270 | 4.319652348285416 | -0.688467 | -23.732 | 5 | 22 | 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
-26.286kcal/mol
Ligand efficiency (LE)
-0.6917kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-7.131
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
38HA
Physicochemical properties
Molecular weight
514.6Da
Lipinski: ≤ 500 Da
LogP (cLogP)
5.18
Lipinski: ≤ 5
Rotatable bonds
9
Conformational strain (MMFF94s)
Strain energy (ΔE)
39.74kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
148.85kcal/mol
Minimised FF energy
109.10kcal/mol
SASA & burial
✓ computed
SASA (unbound)
826.7Ų
Total solvent-accessible surface area of free ligand
BSA total
604.0Ų
Buried surface area upon binding
BSA apolar
502.9Ų
Hydrophobic contacts buried
BSA polar
101.1Ų
Polar contacts buried
Fraction buried
73.1%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
83.3%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-2786.3Ų
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
1384.4Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)