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 medium
Native mixed
SASA done
Strain ΔE
16.1 kcal/mol
Protein clashes
0
Internal clashes
3
Native overlap
contact recall 0.53, Jaccard 0.53, H-bond role recall 0.20
Reason: no major geometry red flags detected
3 intramolecular clashes
56% of hydrophobic surface appears solvent-exposed (10/18 atoms). Partial exposure is common but may limit selectivity and membrane permeability.
EcoTox / ADMET
In-silico prediction only
Fish LC₅₀
Cat. 1 — Very toxic (≤1 mg/L)
Daphnia EC₅₀
Cat. 1 — Very toxic (≤1 mg/L)
Algae IC₅₀
Cat. 1 — Very toxic (≤1 mg/L)
Bioaccum.
Not B (BCF≤2000)
Persistent
No
ADMET alerts (in-silico)
hERG Medium
Ames Clear
DILI Risk
Molecular report
Promising
Reasonable quality metrics. Warrants further investigation.
✓ Excellent LE (-0.937 kcal/mol/HA)
✓ Good fit quality (FQ -8.52)
✓ Deep burial (78% SASA buried)
✓ Lipophilic contacts well-matched (82%)
✗ Moderate strain (16.1 kcal/mol)
✗ Geometry warnings
✗ Internal clashes (7)
Score
-23.423
kcal/mol
LE
-0.937
kcal/mol/HA
Fit Quality
-8.52
FQ (Leeson)
HAC
25
heavy atoms
MW
406
Da
LogP
4.87
cLogP
Final rank
1.5829
rank score
Inter norm
-0.995
normalised
Contacts
10
H-bonds 3
Interaction summary
HBA 2
HY 3
PI 3
CLASH 3
Interaction summary
HBA 2
HY 3
PI 3
CLASH 3
HBD/HBA · H-bonds (geometric)
HBD = ligand donates H · HBA = ligand accepts H · ~ = weak (≥110°). Mode: permissive. Residues: 1.
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: permissive.
| 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 | 10 | Native recall | 0.53 |
| Jaccard | 0.53 | RMSD | - |
| HB strict | 1 | Strict recall | 0.17 |
| HB same residue+role | 1 | HB role recall | 0.20 |
| HB same residue | 1 | HB residue recall | 0.20 |
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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 17 | 1.5828550760938294 | -0.994883 | -23.4228 | 3 | 10 | 10 | 0.53 | 0.20 | - | no | Current |
Molecular metrics
RDKit SASA burial, strain energy (MMFF94s), ligand efficiency and fit quality for this docking pose.
Scoring & efficiency
Docking score
-23.423kcal/mol
Ligand efficiency (LE)
-0.9369kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-8.517
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
25HA
Physicochemical properties
Molecular weight
406.3Da
Lipinski: ≤ 500 Da
LogP (cLogP)
4.87
Lipinski: ≤ 5
Rotatable bonds
5
Conformational strain (MMFF94s)
Strain energy (ΔE)
16.06kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
63.01kcal/mol
Minimised FF energy
46.95kcal/mol
SASA & burial
✓ computed
SASA (unbound)
643.9Ų
Total solvent-accessible surface area of free ligand
BSA total
498.9Ų
Buried surface area upon binding
BSA apolar
406.4Ų
Hydrophobic contacts buried
BSA polar
92.5Ų
Polar contacts buried
Fraction buried
77.5%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
81.5%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-1714.2Ų
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
2179.4Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA
1005.3Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)