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
Promising
SASA cached
Promising and worth follow-up
Binding strong
Geometry high
Native strong
SASA done
Strain ΔE
12.5 kcal/mol
Protein clashes
1
Internal clashes
1
Native overlap
contact recall 0.79, Jaccard 0.65, H-bond role recall 0.44
Reason: no major geometry red flags detected
1 protein-contact clashes
44% of hydrophobic surface appears solvent-exposed (7/16 atoms). Partial exposure is common but may limit selectivity and membrane permeability.
EcoTox / ADMET
In-silico prediction only
Fish LC₅₀
Cat. 3 — Harmful (10–100 mg/L)
Daphnia EC₅₀
Cat. 3 — Harmful (10–100 mg/L)
Algae IC₅₀
Cat. 3 — Harmful (10–100 mg/L)
Bioaccum.
Not B (BCF≤2000)
Persistent
No
ADMET alerts (in-silico)
hERG Low
Ames Clear
DILI Low
Molecular report
Promising
Reasonable quality metrics. Warrants further investigation.
✓ Excellent LE (-1.047 kcal/mol/HA)
✓ Good fit quality (FQ -9.38)
✓ Strong H-bond network (9 bonds)
✓ Deep burial (77% SASA buried)
✗ Moderate strain (12.5 kcal/mol)
✗ Geometry warnings
✗ Internal clashes (7)
Score
-25.133
kcal/mol
LE
-1.047
kcal/mol/HA
Fit Quality
-9.38
FQ (Leeson)
HAC
24
heavy atoms
MW
336
Da
LogP
3.00
cLogP
Final rank
2.6563
rank score
Inter norm
-1.080
normalised
Contacts
14
H-bonds 12
Interaction summary
HBA 9
HY 1
PI 5
CLASH 1
Interaction summary
HBA 9
HY 1
PI 5
CLASH 1
HBD/HBA · H-bonds (geometric)
HBD = ligand donates H · HBA = ligand accepts H · ~ = weak (≥110°). Mode: strict. Residues: 5.
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 | 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 | 0.65 | RMSD | - |
| HB strict | 5 | Strict recall | 0.42 |
| 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 513 | 1.7255116500284249 | -1.06127 | -20.8401 | 2 | 12 | 0 | 0.00 | 0.00 | - | no | Open |
| 507 | 2.2454245298281488 | -0.79818 | -16.7349 | 5 | 9 | 0 | 0.00 | 0.00 | - | no | Open |
| 486 | 2.4557881244034303 | -1.17165 | -27.4838 | 4 | 13 | 0 | 0.00 | 0.00 | - | no | Open |
| 524 | 2.656306600203591 | -1.08008 | -25.1332 | 12 | 14 | 11 | 0.79 | 0.44 | - | no | Current |
| 494 | 3.2626283087821317 | -1.31748 | -28.7197 | 12 | 18 | 0 | 0.00 | 0.00 | - | no | Open |
| 497 | 4.493007696400588 | -1.17875 | -26.5297 | 10 | 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
-25.133kcal/mol
Ligand efficiency (LE)
-1.0472kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-9.385
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
24HA
Physicochemical properties
Molecular weight
336.4Da
Lipinski: ≤ 500 Da
LogP (cLogP)
3.00
Lipinski: ≤ 5
Rotatable bonds
5
Conformational strain (MMFF94s)
Strain energy (ΔE)
12.51kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
64.91kcal/mol
Minimised FF energy
52.40kcal/mol
SASA & burial
✓ computed
SASA (unbound)
500.6Ų
Total solvent-accessible surface area of free ligand
BSA total
384.9Ų
Buried surface area upon binding
BSA apolar
222.1Ų
Hydrophobic contacts buried
BSA polar
162.8Ų
Polar contacts buried
Fraction buried
76.9%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
57.7%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-2044.5Ų
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
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)