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
18.6 kcal/mol
Protein clashes
2
Internal clashes
2
Native overlap
contact recall 0.69, Jaccard 0.47
Reason: no major geometry red flags detected
2 protein-contact clashes
36% of hydrophobic surface appears solvent-exposed (9/25 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
No
ADMET alerts (in-silico)
hERG High
Ames Clear
DILI Risk
Molecular report
Weak
Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-0.622 kcal/mol/HA)
✓ Good fit quality (FQ -6.17)
✓ Deep burial (66% SASA buried)
✓ Lipophilic contacts well-matched (64%)
✗ Moderate strain (18.6 kcal/mol)
✗ Geometry warnings
✗ Many internal clashes (12)
Score
-20.531
kcal/mol
LE
-0.622
kcal/mol/HA
Fit Quality
-6.17
FQ (Leeson)
HAC
33
heavy atoms
MW
475
Da
LogP
4.89
cLogP
Final rank
2.7275
rank score
Inter norm
-0.636
normalised
Contacts
15
H-bonds 2
Interaction summary
HBD 1
HY 7
PI 4
CLASH 2
Interaction summary
HBD 1
HY 7
PI 4
CLASH 2
HBD/HBA · H-bonds (geometric)
HBD = ligand donates H · HBA = ligand accepts H · ~ = weak (≥110°). Mode: strict. Residues: 1.
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 | 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 | 9 | Native recall | 0.69 |
| Jaccard | 0.47 | 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
| Pose | Final rank | Inter norm | Score | HB | CT | CT overlap | CT recall | HB role rec. | RMSD | Excluded | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 495 | 0.7636299668614087 | -0.944298 | -31.6224 | 5 | 18 | 0 | 0.00 | - | - | no | Open |
| 547 | 1.3092080501017846 | -0.748973 | -24.4712 | 3 | 18 | 0 | 0.00 | - | - | no | Open |
| 568 | 2.1136660153511535 | -0.774735 | -23.372 | 2 | 20 | 0 | 0.00 | - | - | no | Open |
| 508 | 2.363635055852463 | -0.896611 | -27.6232 | 10 | 17 | 0 | 0.00 | - | - | no | Open |
| 506 | 2.512933131032401 | -0.972941 | -29.8517 | 9 | 26 | 0 | 0.00 | - | - | no | Open |
| 547 | 2.7275152541986074 | -0.63594 | -20.531 | 2 | 15 | 9 | 0.69 | - | - | no | Current |
| 530 | 3.647484580817899 | -0.738297 | -22.9327 | 4 | 17 | 0 | 0.00 | - | - | no | Open |
| 517 | 3.7491718068183464 | -0.73996 | -23.338 | 12 | 20 | 0 | 0.00 | - | - | no | Open |
| 555 | 4.578227095484919 | -0.730577 | -20.9774 | 4 | 14 | 0 | 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
-20.531kcal/mol
Ligand efficiency (LE)
-0.6222kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-6.173
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
33HA
Physicochemical properties
Molecular weight
474.6Da
Lipinski: ≤ 500 Da
LogP (cLogP)
4.89
Lipinski: ≤ 5
Rotatable bonds
8
Conformational strain (MMFF94s)
Strain energy (ΔE)
18.64kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
84.72kcal/mol
Minimised FF energy
66.08kcal/mol
SASA & burial
✓ computed
SASA (unbound)
760.9Ų
Total solvent-accessible surface area of free ligand
BSA total
505.7Ų
Buried surface area upon binding
BSA apolar
322.7Ų
Hydrophobic contacts buried
BSA polar
182.9Ų
Polar contacts buried
Fraction buried
66.5%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
63.8%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-3154.5Ų
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
1486.2Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)