Molecular metrics status: done
RDKit SASA-based burial metrics are cached.
SASA cached
3D complex viewer
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Protein receptor
Pocket residues
Cofactor context
Docked ligand
Overall assessment
Weak
SASA cached
Weak or marginal quality
Binding strong
Geometry high
Native mixed
SASA done
Strain ΔE
20.6 kcal/mol
Protein clashes
2
Internal clashes
2
Native overlap
contact recall 0.33, Jaccard 0.26, H-bond role recall 0.33
Reason: no major geometry red flags detected
2 protein-contact clashes
60% of hydrophobic surface is solvent-exposed (12/20 atoms). Large non-polar area without protein contacts incurs a desolvation penalty and will reduce binding affinity. Consider truncating or replacing the exposed fragment.
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 Medium
Ames Clear
DILI Risk
Molecular report
Weak
Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-0.803 kcal/mol/HA)
✓ Good fit quality (FQ -7.67)
✓ Strong H-bond network (6 bonds)
✓ Deep burial (75% SASA buried)
✓ Lipophilic contacts well-matched (71%)
✗ High strain energy (20.6 kcal/mol)
✗ Geometry warnings
✗ Internal clashes (8)
Score
-23.288
kcal/mol
LE
-0.803
kcal/mol/HA
Fit Quality
-7.67
FQ (Leeson)
HAC
29
heavy atoms
MW
428
Da
LogP
4.13
cLogP
Final rank
2.3702
rank score
Inter norm
-0.882
normalised
Contacts
13
H-bonds 7
Interaction summary
HBA 6
HY 6
PI 0
CLASH 2
Interaction summary
HBA 6
HY 6
PI 0
CLASH 2
HBD/HBA · H-bonds (geometric)
HBD = ligand donates H · HBA = ligand accepts H · ~ = weak (≥110°). Mode: strict. Residues: 4.
PI · π–π interactions
No pi · π–π interactions detected for this pose.
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 | 3CL9 | Contacts | 21 |
|---|---|---|---|
| Pose | Open native pose | HB | 0 |
| IFP residues |
NDP301
ALA32
ARG97
ASP52
GLY157
ILE45
LEU94
LYS57
MET53
PHE55
PHE56
PHE91
PRO88
SER86
THR180
THR83
TYR162
VAL156
VAL30
VAL31
VAL87
| ||
| Current overlap | 7 | Native recall | 0.33 |
| Jaccard | 0.26 | RMSD | - |
| HB strict | 2 | Strict recall | 0.29 |
| HB same residue+role | 2 | HB role recall | 0.33 |
| HB same residue | 2 | HB residue recall | 0.33 |
Protein summary
511 residues
| Protein target | T09 | Atoms | 8170 |
|---|---|---|---|
| Residues | 511 | Chains | 2 |
| Residue summary | LEU:1064; ARG:840; LYS:572; GLU:570; VAL:528; PHE:460; ILE:456; ALA:440; PRO:420; THR:406; TYR:357; ASP:312; GLN:289; ASN:238; SER:231; GLY:224 | ||
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:NDP301
All stored poses for this docking hit
| Pose | Final rank | Inter norm | Score | HB | CT | CT overlap | CT recall | HB role rec. | RMSD | Excluded | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 120 | 0.3838975461445835 | -1.07679 | -20.459 | 3 | 18 | 0 | 0.00 | 0.00 | - | no | Open |
| 500 | 2.370187323226859 | -0.88212 | -23.2884 | 7 | 13 | 7 | 0.33 | 0.33 | - | no | Current |
| 118 | 2.6329449815392847 | -0.910811 | -24.5174 | 2 | 17 | 12 | 0.57 | 0.00 | - | no | Open |
| 90 | 3.3287066334218705 | -0.964269 | -23.5227 | 7 | 20 | 0 | 0.00 | 0.00 | - | no | Open |
| 506 | 3.3404529615462035 | -0.952543 | -23.435 | 8 | 20 | 0 | 0.00 | 0.00 | - | no | Open |
| 504 | 3.3802376458528895 | -0.933988 | -24.0864 | 11 | 14 | 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
-23.288kcal/mol
Ligand efficiency (LE)
-0.8030kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-7.666
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
29HA
Physicochemical properties
Molecular weight
427.5Da
Lipinski: ≤ 500 Da
LogP (cLogP)
4.13
Lipinski: ≤ 5
Rotatable bonds
6
Conformational strain (MMFF94s)
Strain energy (ΔE)
20.57kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
65.22kcal/mol
Minimised FF energy
44.66kcal/mol
SASA & burial
✓ computed
SASA (unbound)
692.4Ų
Total solvent-accessible surface area of free ligand
BSA total
521.6Ų
Buried surface area upon binding
BSA apolar
371.0Ų
Hydrophobic contacts buried
BSA polar
150.7Ų
Polar contacts buried
Fraction buried
75.3%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
71.1%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-3200.3Ų
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
4428.5Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA
1720.9Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)