Molecular metrics status: done
RDKit SASA-based burial metrics are cached.
SASA cached
3D complex viewer
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Protein receptor
Pocket residues
Cofactor context
Docked ligand
Overall assessment
Reject
SASA cached
Promising but geometrically suspicious
Binding strong
Geometry low
Native strong
SASA done
Strain ΔE
45.6 kcal/mol
Protein clashes
0
Internal clashes
12
Native overlap
contact recall 0.68, Jaccard 0.62, H-bond role recall 0.60
Reason: 12 internal clashes, strain 45.6 kcal/mol
strain ΔE 45.6 kcal/mol
12 intramolecular clashes
45% of hydrophobic surface appears solvent-exposed (13/29 atoms). Partial exposure is common but may limit selectivity and membrane permeability.
EcoTox / ADMET
In-silico prediction only
Fish LC₅₀
Cat. 2 — Toxic (1–10 mg/L)
Daphnia EC₅₀
Cat. 2 — Toxic (1–10 mg/L)
Algae IC₅₀
Cat. 2 — Toxic (1–10 mg/L)
Bioaccum.
Not B (BCF≤2000)
Persistent
No
ADMET alerts (in-silico)
hERG High
Ames Clear
DILI Risk
Molecular report
Reject
Multiple quality flags — this pose should be deprioritised or discarded.
✓ Excellent LE (-0.520 kcal/mol/HA)
✓ Good fit quality (FQ -5.36)
✓ Good H-bonds (4 bonds)
✓ Deep burial (69% SASA buried)
✓ Lipophilic contacts well-matched (93%)
✗ Extreme strain energy (45.6 kcal/mol)
✗ Geometry warnings
✗ Many internal clashes (12)
Score
-19.769
kcal/mol
LE
-0.520
kcal/mol/HA
Fit Quality
-5.36
FQ (Leeson)
HAC
38
heavy atoms
MW
519
Da
LogP
4.03
cLogP
Final rank
2.3583
rank score
Inter norm
-0.649
normalised
Contacts
15
H-bonds 7
Interaction summary
HBD 3
HBA 1
HY 5
PI 1
CLASH 0
Interaction summary
HBD 3
HBA 1
HY 5
PI 1
CLASH 0
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
No clash · clashes detected for this pose.
Native ligand reference
★ reference
Interaction fingerprint calculated directly from the uploaded native ligand without docking. Current H-bond mode: strict.
| Name | 7PXX | Contacts | 19 |
|---|---|---|---|
| Pose | Open native pose | HB | 0 |
| IFP residues |
ARG17
ASP181
GLY225
HIS241
LEU188
LEU226
LEU229
LYS198
MET233
NDP302
PHE113
PRO115
SER111
SER112
SER227
TYR191
TYR194
VAL230
ARG287
| ||
| Current overlap | 13 | Native recall | 0.68 |
| Jaccard | 0.62 | RMSD | - |
| HB strict | 4 | Strict recall | 0.67 |
| HB same residue+role | 3 | HB role recall | 0.60 |
| HB same residue | 3 | HB residue recall | 0.60 |
Protein summary
308 residues
| Protein target | T04 | Atoms | 4210 |
|---|---|---|---|
| Residues | 308 | Chains | 3 |
| 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 44 | 2.3582817165796444 | -0.649086 | -19.7687 | 7 | 15 | 13 | 0.68 | 0.60 | - | no | Current |
Molecular metrics
RDKit SASA burial, strain energy (MMFF94s), ligand efficiency and fit quality for this docking pose.
Scoring & efficiency
Docking score
-19.769kcal/mol
Ligand efficiency (LE)
-0.5202kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-5.363
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
38HA
Physicochemical properties
Molecular weight
518.7Da
Lipinski: ≤ 500 Da
LogP (cLogP)
4.03
Lipinski: ≤ 5
Rotatable bonds
13
Conformational strain (MMFF94s)
Strain energy (ΔE)
45.65kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
160.05kcal/mol
Minimised FF energy
114.40kcal/mol
SASA & burial
✓ computed
SASA (unbound)
841.3Ų
Total solvent-accessible surface area of free ligand
BSA total
578.1Ų
Buried surface area upon binding
BSA apolar
540.0Ų
Hydrophobic contacts buried
BSA polar
38.2Ų
Polar contacts buried
Fraction buried
68.7%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
93.4%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-1890.0Ų
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
1038.5Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)