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 medium
Native strong
SASA done
Strain ΔE
21.2 kcal/mol
Protein clashes
4
Internal clashes
4
Native overlap
contact recall 0.71, Jaccard 0.60, H-bond role recall 0.33
Reason: no major geometry red flags detected
4 protein-contact clashes
4 intramolecular clashes
EcoTox / ADMET
In-silico prediction only
Fish LC₅₀
Cat. 1 — Very toxic (≤1 mg/L)
Daphnia EC₅₀
Cat. 1 — Very toxic (≤1 mg/L)
Algae IC₅₀
Cat. 1 — Very toxic (≤1 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 (-0.818 kcal/mol/HA)
✓ Good fit quality (FQ -7.89)
✓ Good H-bonds (4 bonds)
✓ Deep burial (78% SASA buried)
✓ Lipophilic contacts well-matched (85%)
✗ High strain energy (21.2 kcal/mol)
✗ Geometry warnings
✗ Many internal clashes (11)
Score
-24.534
kcal/mol
LE
-0.818
kcal/mol/HA
Fit Quality
-7.89
FQ (Leeson)
HAC
30
heavy atoms
MW
409
Da
LogP
4.98
cLogP
Final rank
3.5243
rank score
Inter norm
-0.958
normalised
Contacts
15
H-bonds 5
Interaction summary
HBD 1
HBA 3
PC 1
HY 6
PI 3
CLASH 4
Interaction summary
HBD 1
HBA 3
PC 1
HY 6
PI 3
CLASH 4
HBD/HBA · H-bonds (geometric)
HBD = ligand donates H · HBA = ligand accepts H · ~ = weak (≥110°). Mode: strict. Residues: 3.
PC · Polar contacts (possible, no H geometry)
HBD?/HBA? — heavy-atom distance only, H geometry unavailable. May be real H-bonds.
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 | ligand | Contacts | 17 |
|---|---|---|---|
| Pose | Open native pose | HB | 0 |
| IFP residues |
ARG17
GLY225
HIS241
LEU188
LEU226
LEU229
LYS198
MET233
NDP302
PHE113
PRO115
SER111
SER227
TYR191
TYR194
VAL230
ARG287
| ||
| Current overlap | 12 | Native recall | 0.71 |
| Jaccard | 0.60 | RMSD | - |
| HB strict | 2 | Strict recall | 0.29 |
| HB same residue+role | 2 | HB role recall | 0.33 |
| HB same residue | 3 | HB residue recall | 0.60 |
Protein summary
274 residues
| Protein target | T05 | Atoms | 4108 |
|---|---|---|---|
| Residues | 274 | Chains | 2 |
| 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 252 | 1.8484657410477565 | -1.02406 | -26.447 | 4 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 306 | 2.7587280890065067 | -1.0108 | -25.6865 | 4 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 243 | 2.771996727510083 | -0.760311 | -11.5868 | 5 | 19 | 0 | 0.00 | 0.00 | - | no | Open |
| 289 | 3.025607982132919 | -0.867396 | -23.1355 | 8 | 18 | 0 | 0.00 | 0.00 | - | no | Open |
| 244 | 3.5242873499806526 | -0.958256 | -24.534 | 5 | 15 | 12 | 0.71 | 0.33 | - | no | Current |
Molecular metrics
RDKit SASA burial, strain energy (MMFF94s), ligand efficiency and fit quality for this docking pose.
Scoring & efficiency
Docking score
-24.534kcal/mol
Ligand efficiency (LE)
-0.8178kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-7.889
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
30HA
Physicochemical properties
Molecular weight
409.5Da
Lipinski: ≤ 500 Da
LogP (cLogP)
4.98
Lipinski: ≤ 5
Rotatable bonds
6
Conformational strain (MMFF94s)
Strain energy (ΔE)
21.25kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
62.39kcal/mol
Minimised FF energy
41.14kcal/mol
SASA & burial
✓ computed
SASA (unbound)
700.7Ų
Total solvent-accessible surface area of free ligand
BSA total
550.2Ų
Buried surface area upon binding
BSA apolar
468.7Ų
Hydrophobic contacts buried
BSA polar
81.5Ų
Polar contacts buried
Fraction buried
78.5%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
85.2%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-1745.2Ų
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
1038.8Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)