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
15.1 kcal/mol
Protein clashes
4
Internal clashes
10
Native overlap
contact recall 0.79, Jaccard 0.69, H-bond role recall 0.22
Reason: 10 internal clashes
4 protein-contact clashes
10 intramolecular clashes
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 Low
Ames Clear
DILI Risk
Molecular report
Weak
Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-0.871 kcal/mol/HA)
✓ Good fit quality (FQ -8.22)
✓ Good H-bonds (4 bonds)
✓ Deep burial (69% SASA buried)
✓ Lipophilic contacts well-matched (80%)
✗ Moderate strain (15.1 kcal/mol)
✗ Geometry warnings
✗ Minor protein-contact clashes (4)
✗ Many internal clashes (10)
Score
-24.395
kcal/mol
LE
-0.871
kcal/mol/HA
Fit Quality
-8.22
FQ (Leeson)
HAC
28
heavy atoms
MW
408
Da
LogP
4.36
cLogP
Final rank
0.9795
rank score
Inter norm
-0.902
normalised
Contacts
13
H-bonds 9
Interaction summary
HBA 4
HY 2
PI 4
CLASH 0
Interaction summary
HBA 4
HY 2
PI 4
CLASH 0
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
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 | 11 | Native recall | 0.79 |
| Jaccard | 0.69 | RMSD | - |
| HB strict | 3 | Strict recall | 0.25 |
| HB same residue+role | 2 | HB role recall | 0.22 |
| HB same residue | 2 | HB residue recall | 0.25 |
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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 667 | 0.27702236119236995 | -1.15811 | -30.4088 | 4 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 666 | 0.280956076093951 | -1.17112 | -32.4681 | 4 | 20 | 0 | 0.00 | 0.00 | - | no | Open |
| 645 | 0.5207002744452185 | -1.01357 | -27.9962 | 0 | 20 | 0 | 0.00 | 0.00 | - | no | Open |
| 673 | 0.9794964974477434 | -0.901717 | -24.3945 | 9 | 13 | 11 | 0.79 | 0.22 | - | no | Current |
| 647 | 1.0035111429499486 | -0.901451 | -25.5543 | 1 | 17 | 0 | 0.00 | 0.00 | - | no | Open |
| 658 | 2.472374012581643 | -0.966118 | -25.9507 | 4 | 12 | 0 | 0.00 | 0.00 | - | no | Open |
| 660 | 2.982534120422624 | -1.09735 | -27.3518 | 4 | 15 | 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
-24.395kcal/mol
Ligand efficiency (LE)
-0.8712kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-8.225
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
28HA
Physicochemical properties
Molecular weight
407.5Da
Lipinski: ≤ 500 Da
LogP (cLogP)
4.36
Lipinski: ≤ 5
Rotatable bonds
5
Conformational strain (MMFF94s)
Strain energy (ΔE)
15.08kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
52.15kcal/mol
Minimised FF energy
37.07kcal/mol
SASA & burial
✓ computed
SASA (unbound)
651.4Ų
Total solvent-accessible surface area of free ligand
BSA total
452.1Ų
Buried surface area upon binding
BSA apolar
361.8Ų
Hydrophobic contacts buried
BSA polar
90.3Ų
Polar contacts buried
Fraction buried
69.4%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
80.0%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-2222.9Ų
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
770.2Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)