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 strong
SASA done
Strain ΔE
7.8 kcal/mol
Protein clashes
1
Internal clashes
1
Native overlap
contact recall 0.59, Jaccard 0.50, H-bond role recall 0.33
Reason: no major geometry red flags detected
1 protein-contact clashes
EcoTox / ADMET
In-silico prediction only
Fish LC₅₀
Cat. 3 — Harmful (10–100 mg/L)
Daphnia EC₅₀
Cat. 3 — Harmful (10–100 mg/L)
Algae IC₅₀
Cat. 3 — Harmful (10–100 mg/L)
Bioaccum.
Not B (BCF≤2000)
Persistent
No
ADMET alerts (in-silico)
hERG Low
Ames Clear
DILI Low
Molecular report
Promising
Reasonable quality metrics. Warrants further investigation.
✓ Low conformational strain (7.8 kcal/mol)
✓ Excellent LE (-1.145 kcal/mol/HA)
✓ Good fit quality (FQ -10.26)
✓ Good H-bonds (4 bonds)
✓ Deep burial (85% SASA buried)
✓ Lipophilic contacts well-matched (70%)
✗ Geometry warnings
✗ Internal clashes (7)
Score
-27.484
kcal/mol
LE
-1.145
kcal/mol/HA
Fit Quality
-10.26
FQ (Leeson)
HAC
24
heavy atoms
MW
336
Da
LogP
3.00
cLogP
Final rank
2.4558
rank score
Inter norm
-1.172
normalised
Contacts
13
H-bonds 4
Interaction summary
HBA 4
HY 5
PI 3
CLASH 1
Interaction summary
HBA 4
HY 5
PI 3
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 | 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 | 0.50 | RMSD | - |
| HB strict | 2 | Strict recall | 0.29 |
| HB same residue+role | 2 | HB role recall | 0.33 |
| HB same residue | 2 | HB residue recall | 0.40 |
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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 513 | 1.7255116500284249 | -1.06127 | -20.8401 | 2 | 12 | 11 | 0.65 | 0.17 | - | no | Open |
| 507 | 2.2454245298281488 | -0.79818 | -16.7349 | 5 | 9 | 0 | 0.00 | 0.00 | - | no | Open |
| 486 | 2.4557881244034303 | -1.17165 | -27.4838 | 4 | 13 | 10 | 0.59 | 0.33 | - | no | Current |
| 524 | 2.656306600203591 | -1.08008 | -25.1332 | 12 | 14 | 0 | 0.00 | 0.00 | - | no | Open |
| 494 | 3.2626283087821317 | -1.31748 | -28.7197 | 12 | 18 | 0 | 0.00 | 0.00 | - | no | Open |
| 497 | 4.493007696400588 | -1.17875 | -26.5297 | 10 | 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
-27.484kcal/mol
Ligand efficiency (LE)
-1.1452kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-10.263
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
24HA
Physicochemical properties
Molecular weight
336.4Da
Lipinski: ≤ 500 Da
LogP (cLogP)
3.00
Lipinski: ≤ 5
Rotatable bonds
5
Conformational strain (MMFF94s)
Strain energy (ΔE)
7.81kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
60.21kcal/mol
Minimised FF energy
52.40kcal/mol
SASA & burial
✓ computed
SASA (unbound)
570.5Ų
Total solvent-accessible surface area of free ligand
BSA total
484.1Ų
Buried surface area upon binding
BSA apolar
339.4Ų
Hydrophobic contacts buried
BSA polar
144.7Ų
Polar contacts buried
Fraction buried
84.8%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
70.1%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-1553.3Ų
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
1044.4Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)