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 mixed
SASA done
Strain ΔE
18.6 kcal/mol
Protein clashes
1
Internal clashes
1
Native overlap
contact recall 0.52, Jaccard 0.44, H-bond role recall 0.00
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)
0.437
ADMET + ECO + DL
ADMETscore (GDS)
0.490
absorption · distr. · metab.
DLscore
0.435
drug-likeness
P(SAFE)
0.45
GDS classification
ADMET alerts (in-silico)
hERG Low
Ames Clear
DILI Low
Molecular report
Promising
Reasonable quality metrics. Warrants further investigation.
✓ Excellent LE (-0.963 kcal/mol/HA)
✓ Good fit quality (FQ -8.63)
✓ Good H-bonds (5 bonds)
✓ Deep burial (83% SASA buried)
✓ Lipophilic contacts well-matched (63%)
✗ Moderate strain (18.6 kcal/mol)
✗ Geometry warnings
Score
-23.103
kcal/mol
LE
-0.963
kcal/mol/HA
Fit Quality
-8.63
FQ (Leeson)
HAC
24
heavy atoms
MW
367
Da
LogP
3.19
cLogP
Final rank
1.4981
rank score
Inter norm
-1.161
normalised
Contacts
15
H-bonds 5
Interaction summary
HBA 5
HY 8
PI 2
CLASH 1
Interaction summary
HBA 5
HY 8
PI 2
CLASH 1
HBD/HBA · H-bonds (geometric)
HBD = ligand donates H · HBA = ligand accepts H · ~ = weak (≥110°). Mode: strict. Residues: 3.
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 | 5SD8 | Contacts | 21 |
|---|---|---|---|
| Pose | Open native pose | HB | 0 |
| IFP residues |
ALA10
ASN65
ASP22
GLN36
GLU31
GLY117
GLY21
ILE61
ILE8
LEU23
LEU68
NAP201
PHE32
PHE35
PRO62
SER60
THR137
THR57
TYR122
VAL116
VAL9
| ||
| Current overlap | 11 | Native recall | 0.52 |
| Jaccard | 0.44 | 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
200 residues
| Protein target | T02 | Atoms | 3128 |
|---|---|---|---|
| Residues | 200 | Chains | 2 |
| Residue summary | LYS:374; LEU:361; GLU:240; VAL:224; ARG:192; PHE:180; ILE:171; PRO:168; ASN:140; SER:132; TYR:126; GLN:119; ASP:108; MET:102; THR:98; GLY:91 | ||
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:NAP201
All stored poses for this docking hit
| Pose | Final rank | Inter norm | Score | HB | CT | CT overlap | CT recall | HB role rec. | RMSD | Excluded | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 250 | 0.33124369498846573 | -1.29643 | -23.0727 | 5 | 18 | 0 | 0.00 | 0.00 | - | no | Open |
| 306 | 1.4980844275439626 | -1.16076 | -23.1033 | 5 | 15 | 11 | 0.52 | 0.00 | - | no | Current |
| 302 | 2.3012365417379717 | -1.12079 | -20.9957 | 6 | 10 | 0 | 0.00 | 0.00 | - | no | Open |
| 220 | 2.4491462354209257 | -1.17492 | -27.4486 | 11 | 14 | 0 | 0.00 | 0.00 | - | no | Open |
| 246 | 2.5415044901747534 | -1.09194 | -21.3662 | 6 | 14 | 0 | 0.00 | 0.00 | - | no | Open |
| 304 | 3.2694936552292573 | -0.787157 | -13.9191 | 10 | 13 | 0 | 0.00 | 0.00 | - | no | Open |
| 223 | 6.3559024232398045 | -1.30285 | -23.833 | 16 | 18 | 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
-23.103kcal/mol
Ligand efficiency (LE)
-0.9626kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-8.627
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
24HA
Physicochemical properties
Molecular weight
366.5Da
Lipinski: ≤ 500 Da
LogP (cLogP)
3.19
Lipinski: ≤ 5
Rotatable bonds
10
Conformational strain (MMFF94s)
Strain energy (ΔE)
18.60kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
22.84kcal/mol
Minimised FF energy
4.24kcal/mol
SASA & burial
✓ computed
SASA (unbound)
636.1Ų
Total solvent-accessible surface area of free ligand
BSA total
525.6Ų
Buried surface area upon binding
BSA apolar
332.9Ų
Hydrophobic contacts buried
BSA polar
192.8Ų
Polar contacts buried
Fraction buried
82.6%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
63.3%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-1475.2Ų
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
1677.9Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA
609.6Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)