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
18.0 kcal/mol
Protein clashes
2
Internal clashes
2
Native overlap
contact recall 0.48, Jaccard 0.40, H-bond role recall 0.00
Reason: no major geometry red flags detected
2 protein-contact clashes
EcoTox / ADMET
In-silico prediction only
Fish LC₅₀
Cat. 2 — Toxic (1–10 mg/L)
Daphnia EC₅₀
Cat. 1 — Very toxic (≤1 mg/L)
Algae IC₅₀
Cat. 2 — Toxic (1–10 mg/L)
Bioaccum.
Not B (BCF≤2000)
Persistent
No
ADMET alerts (in-silico)
hERG Low
Ames Clear
DILI Risk
Molecular report
Promising
Reasonable quality metrics. Warrants further investigation.
✓ Excellent LE (-0.923 kcal/mol/HA)
✓ Good fit quality (FQ -8.72)
✓ Good H-bonds (3 bonds)
✓ Deep burial (83% SASA buried)
✓ Lipophilic contacts well-matched (71%)
✗ Moderate strain (18.0 kcal/mol)
✗ Geometry warnings
✗ Internal clashes (6)
Score
-25.851
kcal/mol
LE
-0.923
kcal/mol/HA
Fit Quality
-8.72
FQ (Leeson)
HAC
28
heavy atoms
MW
393
Da
LogP
4.58
cLogP
Final rank
3.6092
rank score
Inter norm
-1.000
normalised
Contacts
14
H-bonds 3
Interaction summary
HBA 3
HY 9
PI 3
CLASH 2
Interaction summary
HBA 3
HY 9
PI 3
CLASH 2
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 | 10 | Native recall | 0.48 |
| Jaccard | 0.40 | 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 522 | 3.609225301602353 | -0.999878 | -25.8505 | 3 | 14 | 10 | 0.48 | 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
-25.851kcal/mol
Ligand efficiency (LE)
-0.9232kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-8.716
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
28HA
Physicochemical properties
Molecular weight
393.5Da
Lipinski: ≤ 500 Da
LogP (cLogP)
4.58
Lipinski: ≤ 5
Rotatable bonds
6
Conformational strain (MMFF94s)
Strain energy (ΔE)
18.00kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
108.87kcal/mol
Minimised FF energy
90.88kcal/mol
SASA & burial
✓ computed
SASA (unbound)
637.3Ų
Total solvent-accessible surface area of free ligand
BSA total
526.6Ų
Buried surface area upon binding
BSA apolar
374.9Ų
Hydrophobic contacts buried
BSA polar
151.7Ų
Polar contacts buried
Fraction buried
82.6%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
71.2%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-1542.1Ų
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
612.2Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)