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
38.0 kcal/mol
Protein clashes
0
Internal clashes
14
Native overlap
contact recall 0.62, Jaccard 0.42
Reason: 14 internal clashes
14 intramolecular clashes
38% of hydrophobic surface appears solvent-exposed (9/24 atoms). Partial exposure is common but may limit selectivity and membrane permeability.
EcoTox / ADMET
GDS: SAFE
UL GreenDrugScore ML model
ECOscore
0.282
aquatic tox · BCF · biodeg.
GDS₃ (3-block)
0.302
ADMET + ECO + DL
ADMETscore (GDS)
0.242
absorption · distr. · metab.
DLscore
0.420
drug-likeness
P(SAFE)
0.72
GDS classification
ADMET alerts (in-silico)
hERG High
Ames Clear
DILI Risk
Molecular report
Weak
Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-0.609 kcal/mol/HA)
✓ Good fit quality (FQ -6.04)
✓ Good H-bonds (5 bonds)
✓ Deep burial (69% SASA buried)
✓ Lipophilic contacts well-matched (73%)
✗ Very high strain energy (38.0 kcal/mol)
✗ Geometry warnings
✗ Many internal clashes (14)
Score
-20.105
kcal/mol
LE
-0.609
kcal/mol/HA
Fit Quality
-6.04
FQ (Leeson)
HAC
33
heavy atoms
MW
462
Da
LogP
5.41
cLogP
Final rank
3.4344
rank score
Inter norm
-0.625
normalised
Contacts
14
H-bonds 8
Interaction summary
HBD 1
HBA 4
PC 1
HY 8
PI 2
CLASH 0
Interaction summary
HBD 1
HBA 4
PC 1
HY 8
PI 2
CLASH 0
HBD/HBA · H-bonds (geometric)
HBD = ligand donates H · HBA = ligand accepts H · ~ = weak (≥110°). Mode: strict. Residues: 3.
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
No clash · clashes detected for this pose.
Native ligand reference
★ reference
Interaction fingerprint calculated directly from the uploaded native ligand without docking. Current H-bond mode: strict.
| Name | 6RB5 | Contacts | 13 |
|---|---|---|---|
| Pose | Open native pose | HB | 0 |
| IFP residues |
ASP116
GLU18
GLY112
ILE106
LEU17
MET113
SER109
THR117
THR335
TRP21
TYR110
VAL53
VAL58
| ||
| Current overlap | 8 | Native recall | 0.62 |
| Jaccard | 0.42 | RMSD | - |
| HB strict | 0 | Strict recall | - |
| HB same residue+role | 0 | HB role recall | - |
| HB same residue | 0 | HB residue recall | - |
Protein summary
493 residues
| Protein target | T18 | Atoms | 7550 |
|---|---|---|---|
| Residues | 493 | Chains | 1 |
| Residue summary | VAL:768; LYS:704; LEU:703; ILE:532; GLU:450; THR:434; ARG:408; PHE:400; ALA:390; ASN:350; PRO:350; GLY:336; SER:319; TYR:294; ASP:276; MET:221 | ||
Receptor context
1 kept / 0 excluded
Receptor context filtering: interactions and SASA are computed against protein atoms plus allowed cofactors/ions. Native ligand-like HETATM partners are excluded from scoring.
Kept context 1
Excluded HETATM 0
Kept cofactors / ions
A:FAD501
All stored poses for this docking hit
Molecular metrics
RDKit SASA burial, strain energy (MMFF94s), ligand efficiency and fit quality for this docking pose.
Scoring & efficiency
Docking score
-20.105kcal/mol
Ligand efficiency (LE)
-0.6092kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-6.045
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
33HA
Physicochemical properties
Molecular weight
461.5Da
Lipinski: ≤ 500 Da
LogP (cLogP)
5.41
Lipinski: ≤ 5
Rotatable bonds
7
Conformational strain (MMFF94s)
Strain energy (ΔE)
38.03kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
56.44kcal/mol
Minimised FF energy
18.41kcal/mol
SASA & burial
✓ computed
SASA (unbound)
764.2Ų
Total solvent-accessible surface area of free ligand
BSA total
529.5Ų
Buried surface area upon binding
BSA apolar
384.7Ų
Hydrophobic contacts buried
BSA polar
144.7Ų
Polar contacts buried
Fraction buried
69.3%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
72.7%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-3161.6Ų
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
4076.6Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA
1517.5Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)