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 weak
SASA done
Strain ΔE
13.9 kcal/mol
Protein clashes
7
Internal clashes
8
Native overlap
contact recall 0.22, Jaccard 0.15, H-bond role recall 0.00
Reason: 8 internal clashes
7 protein-contact clashes
8 intramolecular clashes
41% of hydrophobic surface appears solvent-exposed (7/17 atoms). Partial exposure is common but may limit selectivity and membrane permeability.
EcoTox / ADMET
GDS: UNSAFE
UL GreenDrugScore ML model
ECOscore
0.698
aquatic tox · BCF · biodeg.
GDS₃ (3-block)
0.375
ADMET + ECO + DL
ADMETscore (GDS)
0.213
absorption · distr. · metab.
DLscore
0.466
drug-likeness
P(SAFE)
0.14
GDS classification
ADMET alerts (in-silico)
hERG Medium
Ames Clear
DILI Low
Molecular report
Weak
Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-1.338 kcal/mol/HA)
✓ Good fit quality (FQ -12.32)
✓ Strong H-bond network (6 bonds)
✓ Deep burial (97% SASA buried)
✓ Lipophilic contacts well-matched (83%)
✗ Moderate strain (13.9 kcal/mol)
✗ Geometry warnings
✗ Many internal clashes (11)
Score
-34.778
kcal/mol
LE
-1.338
kcal/mol/HA
Fit Quality
-12.32
FQ (Leeson)
HAC
26
heavy atoms
MW
380
Da
LogP
2.83
cLogP
Final rank
4.6870
rank score
Inter norm
-1.326
normalised
Contacts
19
H-bonds 11
Interaction summary
HBD 1
HBA 5
PC 1
HY 2
PI 0
CLASH 8
Interaction summary
HBD 1
HBA 5
PC 1
HY 2
PI 0
CLASH 8
HBD/HBA · H-bonds (geometric)
HBD = ligand donates H · HBA = ligand accepts H · ~ = weak (≥110°). Mode: strict. Residues: 5.
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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 101 | 4.011482696416853 | -0.861072 | -20.3423 | 6 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 91 | 4.686973952576659 | -1.32612 | -34.7777 | 11 | 19 | 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
-34.778kcal/mol
Ligand efficiency (LE)
-1.3376kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-12.324
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
26HA
Physicochemical properties
Molecular weight
379.8Da
Lipinski: ≤ 500 Da
LogP (cLogP)
2.83
Lipinski: ≤ 5
Rotatable bonds
6
Conformational strain (MMFF94s)
Strain energy (ΔE)
13.90kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
-65.27kcal/mol
Minimised FF energy
-79.17kcal/mol
SASA & burial
✓ computed
SASA (unbound)
578.1Ų
Total solvent-accessible surface area of free ligand
BSA total
561.7Ų
Buried surface area upon binding
BSA apolar
465.8Ų
Hydrophobic contacts buried
BSA polar
96.0Ų
Polar contacts buried
Fraction buried
97.2%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
82.9%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-3082.2Ų
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
4064.7Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA
1464.6Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)