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 mixed
SASA done
Strain ΔE
33.3 kcal/mol
Protein clashes
3
Internal clashes
3
Native overlap
contact recall 0.33, Jaccard 0.21, H-bond role recall 0.20
Reason: no major geometry red flags detected
3 protein-contact clashes
3 intramolecular clashes
EcoTox / ADMET
GDS: SAFE
UL GreenDrugScore ML model
ECOscore
0.282
aquatic tox · BCF · biodeg.
GDS₃ (3-block)
0.392
ADMET + ECO + DL
ADMETscore (GDS)
0.386
absorption · distr. · metab.
DLscore
0.469
drug-likeness
P(SAFE)
0.56
GDS classification
ADMET alerts (in-silico)
hERG High
Ames Clear
DILI Risk
Molecular report
Weak
Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-0.922 kcal/mol/HA)
✓ Good fit quality (FQ -9.23)
✓ Good H-bonds (3 bonds)
✓ Deep burial (94% SASA buried)
✓ Lipophilic contacts well-matched (90%)
✗ Very high strain energy (33.3 kcal/mol)
✗ Geometry warnings
✗ Many internal clashes (18)
Score
-31.349
kcal/mol
LE
-0.922
kcal/mol/HA
Fit Quality
-9.23
FQ (Leeson)
HAC
34
heavy atoms
MW
465
Da
LogP
5.34
cLogP
Final rank
3.1749
rank score
Inter norm
-0.981
normalised
Contacts
24
H-bonds 5
Interaction summary
HBA 3
HY 12
PI 0
CLASH 3
Interaction summary
HBA 3
HY 12
PI 0
CLASH 3
HBD/HBA · H-bonds (geometric)
HBD = ligand donates H · HBA = ligand accepts H · ~ = weak (≥110°). Mode: strict. Residues: 1.
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 | 9 | Native recall | 0.33 |
| Jaccard | 0.21 | RMSD | - |
| HB strict | 1 | Strict recall | 0.08 |
| HB same residue+role | 1 | HB role recall | 0.20 |
| HB same residue | 1 | HB residue recall | 0.25 |
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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 9 | 3.174919504718026 | -0.981309 | -31.3492 | 5 | 24 | 9 | 0.33 | 0.20 | - | no | Current |
Molecular metrics
RDKit SASA burial, strain energy (MMFF94s), ligand efficiency and fit quality for this docking pose.
Scoring & efficiency
Docking score
-31.349kcal/mol
Ligand efficiency (LE)
-0.9220kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-9.226
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
34HA
Physicochemical properties
Molecular weight
464.5Da
Lipinski: ≤ 500 Da
LogP (cLogP)
5.34
Lipinski: ≤ 5
Rotatable bonds
6
Conformational strain (MMFF94s)
Strain energy (ΔE)
33.33kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
-11.23kcal/mol
Minimised FF energy
-44.56kcal/mol
SASA & burial
✓ computed
SASA (unbound)
772.7Ų
Total solvent-accessible surface area of free ligand
BSA total
729.7Ų
Buried surface area upon binding
BSA apolar
659.9Ų
Hydrophobic contacts buried
BSA polar
69.9Ų
Polar contacts buried
Fraction buried
94.4%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
90.4%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-3277.7Ų
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
4064.7Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA
1489.8Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)