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
22.2 kcal/mol
Protein clashes
2
Internal clashes
2
Native overlap
contact recall 0.59, Jaccard 0.48, H-bond role recall 0.50
Reason: no major geometry red flags detected
2 protein-contact clashes
50% of hydrophobic surface appears solvent-exposed (6/12 atoms). Partial exposure is common but may limit selectivity and membrane permeability.
EcoTox / ADMET
In-silico prediction only
Fish LC₅₀
Not classified (>100 mg/L)
Daphnia EC₅₀
Not classified (>100 mg/L)
Algae IC₅₀
Not classified (>100 mg/L)
Bioaccum.
Not B (BCF≤2000)
Persistent
No
ADMET alerts (in-silico)
hERG Low
Ames Clear
DILI Low
Molecular report
Weak
Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-1.307 kcal/mol/HA)
✓ Good fit quality (FQ -11.35)
✓ Good H-bonds (5 bonds)
✓ Deep burial (87% SASA buried)
✓ Lipophilic contacts well-matched (69%)
✗ High strain energy (22.2 kcal/mol)
✗ Geometry warnings
✗ Internal clashes (6)
Score
-28.761
kcal/mol
LE
-1.307
kcal/mol/HA
Fit Quality
-11.35
FQ (Leeson)
HAC
22
heavy atoms
MW
341
Da
LogP
1.09
cLogP
Final rank
2.0876
rank score
Inter norm
-1.294
normalised
Contacts
14
H-bonds 8
Interaction summary
HBD 3
HBA 2
HY 3
PI 1
CLASH 2
Interaction summary
HBD 3
HBA 2
HY 3
PI 1
CLASH 2
HBD/HBA · H-bonds (geometric)
HBD = ligand donates H · HBA = ligand accepts H · ~ = weak (≥110°). Mode: strict. Residues: 4.
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 | ligand | Contacts | 17 |
|---|---|---|---|
| Pose | Open native pose | HB | 0 |
| IFP residues |
ARG17
GLY225
HIS241
LEU188
LEU226
LEU229
LYS198
MET233
NDP302
PHE113
PRO115
SER111
SER227
TYR191
TYR194
VAL230
ARG287
| ||
| Current overlap | 10 | Native recall | 0.59 |
| Jaccard | 0.48 | RMSD | - |
| HB strict | 3 | Strict recall | 0.43 |
| HB same residue+role | 3 | HB role recall | 0.50 |
| HB same residue | 3 | HB residue recall | 0.60 |
Protein summary
274 residues
| Protein target | T05 | Atoms | 4108 |
|---|---|---|---|
| Residues | 274 | Chains | 2 |
| 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 402 | 1.626499043761604 | -1.37094 | -30.1527 | 6 | 14 | 0 | 0.00 | 0.00 | - | no | Open |
| 388 | 1.6518041180779013 | -1.37003 | -30.346 | 7 | 14 | 0 | 0.00 | 0.00 | - | no | Open |
| 300 | 2.0875862514939527 | -1.29433 | -28.7606 | 8 | 14 | 10 | 0.59 | 0.50 | - | no | Current |
| 378 | 2.3075074574600802 | -1.36833 | -30.0855 | 6 | 14 | 0 | 0.00 | 0.00 | - | no | Open |
| 376 | 2.606219346550542 | -1.13545 | -26.0457 | 10 | 17 | 0 | 0.00 | 0.00 | - | no | Open |
| 450 | 2.8599754316936856 | -1.28494 | -28.9186 | 9 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 288 | 3.0559467618395817 | -1.44185 | -31.3269 | 8 | 19 | 0 | 0.00 | 0.00 | - | no | Open |
| 282 | 4.254727390078342 | -1.16966 | -27.913 | 13 | 13 | 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
-28.761kcal/mol
Ligand efficiency (LE)
-1.3073kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-11.350
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
22HA
Physicochemical properties
Molecular weight
341.4Da
Lipinski: ≤ 500 Da
LogP (cLogP)
1.09
Lipinski: ≤ 5
Rotatable bonds
6
Conformational strain (MMFF94s)
Strain energy (ΔE)
22.23kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
-73.78kcal/mol
Minimised FF energy
-96.02kcal/mol
SASA & burial
✓ computed
SASA (unbound)
568.1Ų
Total solvent-accessible surface area of free ligand
BSA total
496.0Ų
Buried surface area upon binding
BSA apolar
341.5Ų
Hydrophobic contacts buried
BSA polar
154.5Ų
Polar contacts buried
Fraction buried
87.3%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
68.9%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-1547.0Ų
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
1034.6Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)