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
Weak or marginal quality
Binding strong
Geometry high
Native strong
SASA done
Strain ΔE
23.3 kcal/mol
Protein clashes
1
Internal clashes
1
Native overlap
contact recall 0.88, Jaccard 0.79, H-bond role recall 0.45
Reason: no major geometry red flags detected
1 protein-contact clashes
70% of hydrophobic surface is solvent-exposed (16/23 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. 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 Medium
Ames Clear
DILI Low
Molecular report
Weak
Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-0.701 kcal/mol/HA)
✓ Good fit quality (FQ -6.69)
✓ Good H-bonds (5 bonds)
✓ Deep burial (67% SASA buried)
✓ Lipophilic contacts well-matched (80%)
✗ High strain energy (23.3 kcal/mol)
✗ Geometry warnings
✗ Many internal clashes (14)
Score
-20.329
kcal/mol
LE
-0.701
kcal/mol/HA
Fit Quality
-6.69
FQ (Leeson)
HAC
29
heavy atoms
MW
397
Da
LogP
3.64
cLogP
Final rank
3.7914
rank score
Inter norm
-0.959
normalised
Contacts
17
H-bonds 8
Interaction summary
HBD 1
HBA 4
HY 4
PI 1
CLASH 1
Interaction summary
HBD 1
HBA 4
HY 4
PI 1
CLASH 1
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 | 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 | 0.79 | RMSD | - |
| HB strict | 4 | Strict recall | 0.31 |
| HB same residue+role | 5 | HB role recall | 0.45 |
| 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 376 | 3.0386066159493392 | -0.850471 | -17.8845 | 8 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 297 | 3.605093104015848 | -0.794204 | -18.4183 | 6 | 14 | 0 | 0.00 | 0.00 | - | no | Open |
| 185 | 3.7913852384024302 | -0.958573 | -20.3291 | 8 | 17 | 15 | 0.88 | 0.45 | - | no | Current |
| 277 | 4.649181311495193 | -0.876009 | -22.4539 | 6 | 16 | 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
-20.329kcal/mol
Ligand efficiency (LE)
-0.7010kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-6.692
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
29HA
Physicochemical properties
Molecular weight
397.5Da
Lipinski: ≤ 500 Da
LogP (cLogP)
3.64
Lipinski: ≤ 5
Rotatable bonds
7
Conformational strain (MMFF94s)
Strain energy (ΔE)
23.25kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
41.15kcal/mol
Minimised FF energy
17.89kcal/mol
SASA & burial
✓ computed
SASA (unbound)
672.8Ų
Total solvent-accessible surface area of free ligand
BSA total
452.2Ų
Buried surface area upon binding
BSA apolar
362.6Ų
Hydrophobic contacts buried
BSA polar
89.6Ų
Polar contacts buried
Fraction buried
67.2%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
80.2%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-2315.6Ų
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
2417.4Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA
660.4Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)