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
39.8 kcal/mol
Protein clashes
0
Internal clashes
16
Native overlap
contact recall 0.74, Jaccard 0.70, H-bond role recall 0.80
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 Medium
Ames Clear
DILI Low
Molecular report
Weak
Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-0.974 kcal/mol/HA)
✓ Good fit quality (FQ -9.83)
✓ Strong H-bond network (6 bonds)
✓ Deep burial (69% SASA buried)
✓ Lipophilic contacts well-matched (80%)
✗ Very high strain energy (39.8 kcal/mol)
✗ Geometry warnings
✗ Many internal clashes (16)
Score
-34.099
kcal/mol
LE
-0.974
kcal/mol/HA
Fit Quality
-9.83
FQ (Leeson)
HAC
35
heavy atoms
MW
479
Da
LogP
2.03
cLogP
Final rank
2.1878
rank score
Inter norm
-1.022
normalised
Contacts
15
H-bonds 6
Interaction summary
HBD 3
HBA 3
HY 7
PI 3
CLASH 0
Interaction summary
HBD 3
HBA 3
HY 7
PI 3
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 | 7PXX | Contacts | 19 |
|---|---|---|---|
| Pose | Open native pose | HB | 0 |
| IFP residues |
ARG17
ASP181
GLY225
HIS241
LEU188
LEU226
LEU229
LYS198
MET233
NDP302
PHE113
PRO115
SER111
SER112
SER227
TYR191
TYR194
VAL230
ARG287
| ||
| Current overlap | 14 | Native recall | 0.74 |
| Jaccard | 0.70 | RMSD | - |
| HB strict | 5 | Strict recall | 0.83 |
| HB same residue+role | 4 | HB role recall | 0.80 |
| HB same residue | 4 | HB residue recall | 0.80 |
Protein summary
308 residues
| Protein target | T04 | Atoms | 4210 |
|---|---|---|---|
| Residues | 308 | Chains | 3 |
| Residue summary | LEU:494; ALA:421; ARG:384; VAL:368; THR:295; TYR:231; SER:198; PRO:196; ILE:190; LYS:176; ASN:154; GLU:150; GLY:126; PHE:120; HIS:119; ASP:108 | ||
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:NDP302
All stored poses for this docking hit
| Pose | Final rank | Inter norm | Score | HB | CT | CT overlap | CT recall | HB role rec. | RMSD | Excluded | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 9 | 2.187825845667926 | -1.02172 | -34.0995 | 6 | 15 | 14 | 0.74 | 0.80 | - | no | Current |
Molecular metrics
RDKit SASA burial, strain energy (MMFF94s), ligand efficiency and fit quality for this docking pose.
Scoring & efficiency
Docking score
-34.099kcal/mol
Ligand efficiency (LE)
-0.9743kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-9.827
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
35HA
Physicochemical properties
Molecular weight
478.6Da
Lipinski: ≤ 500 Da
LogP (cLogP)
2.03
Lipinski: ≤ 5
Rotatable bonds
9
Conformational strain (MMFF94s)
Strain energy (ΔE)
39.82kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
27.29kcal/mol
Minimised FF energy
-12.53kcal/mol
SASA & burial
✓ computed
SASA (unbound)
803.3Ų
Total solvent-accessible surface area of free ligand
BSA total
551.0Ų
Buried surface area upon binding
BSA apolar
441.1Ų
Hydrophobic contacts buried
BSA polar
109.9Ų
Polar contacts buried
Fraction buried
68.6%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
80.1%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-1808.7Ų
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
2179.4Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA
1028.4Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)