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 weak
SASA done
Strain ΔE
15.2 kcal/mol
Protein clashes
2
Internal clashes
2
Native overlap
contact recall 0.22, Jaccard 0.15, H-bond role recall 0.00
Reason: no major geometry red flags detected
2 protein-contact clashes
44% of hydrophobic surface appears solvent-exposed (8/18 atoms). Partial exposure is common but may limit selectivity and membrane permeability.
EcoTox / ADMET
In-silico prediction only
Fish LC₅₀
Not classified (>100 mg/L)
Daphnia EC₅₀
Not classified (>100 mg/L)
Algae IC₅₀
Cat. 3 — Harmful (10–100 mg/L)
Bioaccum.
Not B (BCF≤2000)
Persistent
No
ADMET alerts (in-silico)
hERG Medium
Ames Clear
DILI Low
Molecular report
Promising
Reasonable quality metrics. Warrants further investigation.
✓ Excellent LE (-1.041 kcal/mol/HA)
✓ Good fit quality (FQ -9.47)
✓ Good H-bonds (3 bonds)
✓ Deep burial (97% SASA buried)
✓ Lipophilic contacts well-matched (84%)
✗ Moderate strain (15.2 kcal/mol)
✗ Geometry warnings
✗ Internal clashes (6)
Score
-26.033
kcal/mol
LE
-1.041
kcal/mol/HA
Fit Quality
-9.47
FQ (Leeson)
HAC
25
heavy atoms
MW
341
Da
LogP
2.27
cLogP
Final rank
1.5963
rank score
Inter norm
-1.278
normalised
Contacts
20
H-bonds 8
Interaction summary
HBA 3
PC 2
HY 6
PI 0
CLASH 2
Interaction summary
HBA 3
PC 2
HY 6
PI 0
CLASH 2
HBD/HBA · H-bonds (geometric)
HBD = ligand donates H · HBA = ligand accepts H · ~ = weak (≥110°). Mode: strict. Residues: 2.
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
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 | 2WOV | Contacts | 27 |
|---|---|---|---|
| Pose | Open native pose | HB | 0 |
| IFP residues |
ALA284
ALA365
ARG222
ARG228
ARG287
ASN223
ASN254
GLN165
GLU202
GLY195
GLY196
GLY197
GLY286
ILE199
ILE285
LEU227
LEU334
LYS60
MET333
NDP800
PHE198
PHE367
PRO167
SER200
TYR221
VAL194
VAL366
| ||
| Current overlap | 6 | Native recall | 0.22 |
| Jaccard | 0.15 | RMSD | - |
| HB strict | 0 | Strict recall | 0.00 |
| HB same residue+role | 0 | HB role recall | 0.00 |
| HB same residue | 0 | HB residue recall | 0.00 |
Protein summary
493 residues
| Protein target | T19 | Atoms | 7541 |
|---|---|---|---|
| Residues | 493 | Chains | 1 |
| Residue summary | VAL:768; LYS:704; LEU:703; ILE:532; GLU:450; THR:434; ARG:408; PHE:400; ALA:390; ASN:350; PRO:350; GLY:336; SER:330; TYR:294; ASP:264; MET:221 | ||
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
C:NDP800
All stored poses for this docking hit
| Pose | Final rank | Inter norm | Score | HB | CT | CT overlap | CT recall | HB role rec. | RMSD | Excluded | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 98 | 1.5963089843691398 | -1.27754 | -26.0329 | 8 | 20 | 6 | 0.22 | 0.00 | - | no | Current |
Molecular metrics
RDKit SASA burial, strain energy (MMFF94s), ligand efficiency and fit quality for this docking pose.
Scoring & efficiency
Docking score
-26.033kcal/mol
Ligand efficiency (LE)
-1.0413kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-9.467
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
25HA
Physicochemical properties
Molecular weight
341.4Da
Lipinski: ≤ 500 Da
LogP (cLogP)
2.27
Lipinski: ≤ 5
Rotatable bonds
3
Conformational strain (MMFF94s)
Strain energy (ΔE)
15.24kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
63.65kcal/mol
Minimised FF energy
48.41kcal/mol
SASA & burial
✓ computed
SASA (unbound)
606.5Ų
Total solvent-accessible surface area of free ligand
BSA total
585.8Ų
Buried surface area upon binding
BSA apolar
490.8Ų
Hydrophobic contacts buried
BSA polar
95.0Ų
Polar contacts buried
Fraction buried
96.6%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
83.8%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-3110.5Ų
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
4064.7Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA
1465.8Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)