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
32.6 kcal/mol
Protein clashes
0
Internal clashes
16
Native overlap
contact recall 0.93, Jaccard 0.81, H-bond role recall 0.44
Reason: 16 internal clashes
16 intramolecular clashes
EcoTox / ADMET
In-silico prediction only
Fish LC₅₀
Not classified (>100 mg/L)
Daphnia EC₅₀
Not classified (>100 mg/L)
Algae IC₅₀
Not classified (>100 mg/L)
Bioaccum.
Not B (BCF≤2000)
Persistent
No
ADMET alerts (in-silico)
hERG Low
Ames Clear
DILI Low
Molecular report
Weak
Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-0.881 kcal/mol/HA)
✓ Good fit quality (FQ -8.50)
✓ Good H-bonds (4 bonds)
✓ Deep burial (68% SASA buried)
✓ Lipophilic contacts well-matched (83%)
✗ Very high strain energy (32.6 kcal/mol)
✗ Geometry warnings
✗ Many internal clashes (16)
Score
-26.438
kcal/mol
LE
-0.881
kcal/mol/HA
Fit Quality
-8.50
FQ (Leeson)
HAC
30
heavy atoms
MW
428
Da
LogP
0.53
cLogP
Final rank
4.5593
rank score
Inter norm
-0.808
normalised
Contacts
15
H-bonds 6
Interaction summary
HBD 1
HBA 3
HY 3
PI 2
CLASH 0
Interaction summary
HBD 1
HBA 3
HY 3
PI 2
CLASH 0
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
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 | 3K7O | Contacts | 14 |
|---|---|---|---|
| Pose | Open native pose | HB | 0 |
| IFP residues |
ARG137
ARG141
ASN103
HIS102
HIS138
ASP10
CYS69
GLY70
GLY74
HIS11
ILE73
PRO12
SER71
TYR46
| ||
| Current overlap | 13 | Native recall | 0.93 |
| Jaccard | 0.81 | RMSD | - |
| HB strict | 4 | Strict recall | 0.33 |
| HB same residue+role | 4 | HB role recall | 0.44 |
| HB same residue | 4 | HB residue recall | 0.50 |
Protein summary
305 residues
| Protein target | T21 | Atoms | 4646 |
|---|---|---|---|
| Residues | 305 | Chains | 2 |
| Residue summary | ARG:576; ILE:532; VAL:512; GLU:420; ALA:360; PHE:240; HIS:238; LYS:220; THR:210; LEU:190; PRO:168; TYR:168; GLY:154; SER:154; ASP:144; ASN:112 | ||
All stored poses for this docking hit
| Pose | Final rank | Inter norm | Score | HB | CT | CT overlap | CT recall | HB role rec. | RMSD | Excluded | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 100 | 1.5645178525475796 | -0.998574 | -30.9198 | 4 | 17 | 0 | 0.00 | 0.00 | - | no | Open |
| 68 | 4.559325345752987 | -0.808131 | -26.4384 | 6 | 15 | 13 | 0.93 | 0.44 | - | no | Current |
Molecular metrics
RDKit SASA burial, strain energy (MMFF94s), ligand efficiency and fit quality for this docking pose.
Scoring & efficiency
Docking score
-26.438kcal/mol
Ligand efficiency (LE)
-0.8813kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-8.501
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
30HA
Physicochemical properties
Molecular weight
427.9Da
Lipinski: ≤ 500 Da
LogP (cLogP)
0.53
Lipinski: ≤ 5
Rotatable bonds
7
Conformational strain (MMFF94s)
Strain energy (ΔE)
32.56kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
269.31kcal/mol
Minimised FF energy
236.75kcal/mol
SASA & burial
✓ computed
SASA (unbound)
685.1Ų
Total solvent-accessible surface area of free ligand
BSA total
463.5Ų
Buried surface area upon binding
BSA apolar
384.8Ų
Hydrophobic contacts buried
BSA polar
78.7Ų
Polar contacts buried
Fraction buried
67.7%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
83.0%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-2249.3Ų
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
2482.0Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA
834.5Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)