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
Weak or marginal quality
Binding strong
Geometry high
Native strong
SASA done
Strain ΔE
22.7 kcal/mol
Protein clashes
1
Internal clashes
1
Native overlap
contact recall 0.75, Jaccard 0.50, H-bond role recall 1.00
Reason: no major geometry red flags detected
1 protein-contact clashes
EcoTox / ADMET
GDS: UNSAFE
UL GreenDrugScore ML model
ECOscore
0.282
aquatic tox · BCF · biodeg.
GDS₃ (3-block)
0.338
ADMET + ECO + DL
ADMETscore (GDS)
0.318
absorption · distr. · metab.
DLscore
0.407
drug-likeness
P(SAFE)
0.05
GDS classification
ADMET alerts (in-silico)
hERG Medium
Ames Clear
DILI Risk
Molecular report
Weak
Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-0.624 kcal/mol/HA)
✓ Good fit quality (FQ -5.89)
✓ Deep burial (80% SASA buried)
✓ Lipophilic contacts well-matched (76%)
✗ High strain energy (22.7 kcal/mol)
✗ Geometry warnings
✗ Internal clashes (9)
Score
-17.473
kcal/mol
LE
-0.624
kcal/mol/HA
Fit Quality
-5.89
FQ (Leeson)
HAC
28
heavy atoms
MW
384
Da
LogP
4.16
cLogP
Final rank
1.8863
rank score
Inter norm
-0.844
normalised
Contacts
15
H-bonds 3
Interaction summary
HBD 1
HBA 1
HY 6
PI 2
CLASH 1
Interaction summary
HBD 1
HBA 1
HY 6
PI 2
CLASH 1
HBD/HBA · H-bonds (geometric)
HBD = ligand donates H · HBA = ligand accepts H · ~ = weak (≥110°). Mode: strict. Residues: 2.
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 | 5S9T | Contacts | 12 |
|---|---|---|---|
| Pose | Open native pose | HB | 0 |
| IFP residues |
ALA365
ARG228
ARG331
GLY229
LEU332
LEU334
MET333
PHE198
PHE230
SER364
THR374
VAL366
| ||
| Current overlap | 9 | Native recall | 0.75 |
| Jaccard | 0.50 | RMSD | - |
| HB strict | 1 | Strict recall | 1.00 |
| HB same residue+role | 1 | HB role recall | 1.00 |
| HB same residue | 1 | HB residue recall | 1.00 |
Protein summary
1033 residues
| Protein target | T17 | Atoms | 15160 |
|---|---|---|---|
| Residues | 1033 | Chains | 2 |
| Residue summary | VAL:1536; LEU:1387; LYS:1386; ILE:1064; GLU:900; THR:868; ARG:816; PHE:800; ALA:780; ASN:700; PRO:686; GLY:672; SER:616; TYR:588; ASP:528; MET:408 | ||
Receptor context
2 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 2
Excluded HETATM 0
Kept cofactors / ions
A:FAD501
B:FAD501
All stored poses for this docking hit
| Pose | Final rank | Inter norm | Score | HB | CT | CT overlap | CT recall | HB role rec. | RMSD | Excluded | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 483 | 1.0853100332132994 | -1.15783 | -26.9741 | 5 | 17 | 0 | 0.00 | 0.00 | - | no | Open |
| 533 | 1.3030885157662433 | -0.984884 | -24.6447 | 3 | 20 | 0 | 0.00 | 0.00 | - | no | Open |
| 539 | 1.3153312150478562 | -0.956507 | -24.115 | 5 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 468 | 1.4983376621522455 | -1.21454 | -29.8472 | 7 | 21 | 0 | 0.00 | 0.00 | - | no | Open |
| 487 | 1.829623080713065 | -0.906153 | -22.6394 | 2 | 19 | 0 | 0.00 | 0.00 | - | no | Open |
| 522 | 1.886285713477351 | -0.843689 | -17.4728 | 3 | 15 | 9 | 0.75 | 1.00 | - | no | Current |
| 527 | 2.9175440723674373 | -1.05324 | -24.3241 | 4 | 20 | 0 | 0.00 | 0.00 | - | no | Open |
| 456 | 3.0916468248736995 | -1.03596 | -27.5073 | 4 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
Molecular metrics
RDKit SASA burial, strain energy (MMFF94s), ligand efficiency and fit quality for this docking pose.
Scoring & efficiency
Docking score
-17.473kcal/mol
Ligand efficiency (LE)
-0.6240kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-5.891
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
28HA
Physicochemical properties
Molecular weight
384.5Da
Lipinski: ≤ 500 Da
LogP (cLogP)
4.16
Lipinski: ≤ 5
Rotatable bonds
5
Conformational strain (MMFF94s)
Strain energy (ΔE)
22.66kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
101.45kcal/mol
Minimised FF energy
78.79kcal/mol
SASA & burial
✓ computed
SASA (unbound)
670.3Ų
Total solvent-accessible surface area of free ligand
BSA total
533.9Ų
Buried surface area upon binding
BSA apolar
403.8Ų
Hydrophobic contacts buried
BSA polar
130.1Ų
Polar contacts buried
Fraction buried
79.6%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
75.6%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-6513.9Ų
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
8063.1Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA
2086.2Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)