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 medium
Native mixed
SASA done
Strain ΔE
2.1 kcal/mol
Protein clashes
1
Internal clashes
3
Native overlap
contact recall 0.42, Jaccard 0.42, H-bond role recall 0.20
Reason: no major geometry red flags detected
1 protein-contact clashes
3 intramolecular clashes
EcoTox / ADMET
GDS: UNSAFE
UL GreenDrugScore ML model
ECOscore
0.485
aquatic tox · BCF · biodeg.
GDS₃ (3-block)
0.534
ADMET + ECO + DL
ADMETscore (GDS)
0.616
absorption · distr. · metab.
DLscore
0.420
drug-likeness
P(SAFE)
0.10
GDS classification
ADMET alerts (in-silico)
hERG Low
Ames Clear
DILI Low
Molecular report
Promising
Reasonable quality metrics. Warrants further investigation.
✓ Low conformational strain (2.1 kcal/mol)
✓ Excellent LE (-2.095 kcal/mol/HA)
✓ Good fit quality (FQ -13.86)
✓ Deep burial (95% SASA buried)
✓ Lipophilic contacts well-matched (80%)
✗ Geometry warnings
✗ Internal clashes (6)
Score
-25.136
kcal/mol
LE
-2.095
kcal/mol/HA
Fit Quality
-13.86
FQ (Leeson)
HAC
12
heavy atoms
MW
225
Da
LogP
1.69
cLogP
Final rank
0.1631
rank score
Inter norm
-2.095
normalised
Contacts
8
H-bonds 1
Interaction summary
HBA 1
HY 2
PI 1
CLASH 3
Interaction summary
HBA 1
HY 2
PI 1
CLASH 3
HBD/HBA · H-bonds (geometric)
HBD = ligand donates H · HBA = ligand accepts H · ~ = weak (≥110°). Mode: permissive. Residues: 1.
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: permissive.
| 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 | 8 | Native recall | 0.42 |
| Jaccard | 0.42 | RMSD | - |
| HB strict | 1 | Strict recall | 0.17 |
| HB same residue+role | 1 | HB role recall | 0.20 |
| HB same residue | 1 | HB residue recall | 0.20 |
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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 644 | 0.1631401924028917 | -2.09469 | -25.1363 | 1 | 8 | 8 | 0.42 | 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
-25.136kcal/mol
Ligand efficiency (LE)
-2.0947kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-13.857
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
12HA
Physicochemical properties
Molecular weight
225.0Da
Lipinski: ≤ 500 Da
LogP (cLogP)
1.69
Lipinski: ≤ 5
Rotatable bonds
0
Conformational strain (MMFF94s)
Strain energy (ΔE)
2.10kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
-35.44kcal/mol
Minimised FF energy
-37.54kcal/mol
SASA & burial
✓ computed
SASA (unbound)
341.1Ų
Total solvent-accessible surface area of free ligand
BSA total
324.2Ų
Buried surface area upon binding
BSA apolar
259.9Ų
Hydrophobic contacts buried
BSA polar
64.3Ų
Polar contacts buried
Fraction buried
95.1%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
80.2%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-1430.5Ų
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
2179.4Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA
1023.6Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)