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
Weak
SASA cached
Promising but geometrically suspicious
Binding strong
Geometry low
Native strong
SASA done
Strain ΔE
36.2 kcal/mol
Protein clashes
6
Internal clashes
6
Native overlap
contact recall 0.88, Jaccard 0.75, H-bond role recall 0.55
Reason: 6 internal clashes
6 protein-contact clashes
6 intramolecular clashes
67% of hydrophobic surface is solvent-exposed (14/21 atoms). Large non-polar area without protein contacts incurs a desolvation penalty and will reduce binding affinity. Consider truncating or replacing the exposed fragment.
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 (-0.418 kcal/mol/HA)
✓ Good fit quality (FQ -4.18)
✓ Strong H-bond network (8 bonds)
✓ Deep burial (70% SASA buried)
✓ Lipophilic contacts well-matched (84%)
✗ Very high strain energy (36.2 kcal/mol)
✗ Geometry warnings
✗ Many internal clashes (16)
Score
-14.204
kcal/mol
LE
-0.418
kcal/mol/HA
Fit Quality
-4.18
FQ (Leeson)
HAC
34
heavy atoms
MW
490
Da
LogP
5.00
cLogP
Final rank
4.4027
rank score
Inter norm
-0.711
normalised
Contacts
18
H-bonds 12
Interaction summary
HBD 1
HBA 7
HY 2
PI 2
CLASH 6
Interaction summary
HBD 1
HBA 7
HY 2
PI 2
CLASH 6
HBD/HBA · H-bonds (geometric)
HBD = ligand donates H · HBA = ligand accepts H · ~ = weak (≥110°). Mode: strict. Residues: 6.
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 | 6FXW | Contacts | 17 |
|---|---|---|---|
| Pose | Open native pose | HB | 0 |
| IFP residues |
ALA15
ARG116
ARG140
ARG144
ASN106
ASP13
CYS72
GLY73
GLY75
GLY77
HIS105
HIS14
HIS141
ILE76
LEU101
THR74
TYR49
| ||
| Current overlap | 15 | Native recall | 0.88 |
| Jaccard | 0.75 | RMSD | - |
| HB strict | 7 | Strict recall | 0.54 |
| HB same residue+role | 6 | HB role recall | 0.55 |
| HB same residue | 6 | HB residue recall | 0.55 |
Protein summary
155 residues
| Protein target | T10 | Atoms | 4590 |
|---|---|---|---|
| Residues | 155 | Chains | 1 |
| Residue summary | ILE:494; ARG:384; ALA:360; VAL:352; LEU:304; GLU:300; THR:280; MET:272; LYS:220; ASP:216; TYR:210; HIS:204; GLY:182; SER:176; GLN:170; ASN:140 | ||
All stored poses for this docking hit
| Pose | Final rank | Inter norm | Score | HB | CT | CT overlap | CT recall | HB role rec. | RMSD | Excluded | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 435 | 2.0460325976516107 | -0.767565 | -14.7222 | 4 | 22 | 0 | 0.00 | 0.00 | - | no | Open |
| 378 | 3.5630672438775015 | -0.742341 | -14.7026 | 4 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 479 | 4.359498943658783 | -0.689256 | -18.4486 | 4 | 17 | 0 | 0.00 | 0.00 | - | no | Open |
| 322 | 4.402658225267469 | -0.711147 | -14.2041 | 12 | 18 | 15 | 0.88 | 0.55 | - | no | Current |
Molecular metrics
RDKit SASA burial, strain energy (MMFF94s), ligand efficiency and fit quality for this docking pose.
Scoring & efficiency
Docking score
-14.204kcal/mol
Ligand efficiency (LE)
-0.4178kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-4.180
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
34HA
Physicochemical properties
Molecular weight
489.9Da
Lipinski: ≤ 500 Da
LogP (cLogP)
5.00
Lipinski: ≤ 5
Rotatable bonds
7
Conformational strain (MMFF94s)
Strain energy (ΔE)
36.24kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
87.56kcal/mol
Minimised FF energy
51.31kcal/mol
SASA & burial
✓ computed
SASA (unbound)
731.8Ų
Total solvent-accessible surface area of free ligand
BSA total
509.6Ų
Buried surface area upon binding
BSA apolar
428.0Ų
Hydrophobic contacts buried
BSA polar
81.6Ų
Polar contacts buried
Fraction buried
69.6%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
84.0%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-2294.4Ų
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
2417.4Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA
742.5Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)