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 medium
Native strong
SASA done
Strain ΔE
38.7 kcal/mol
Protein clashes
2
Internal clashes
2
Native overlap
contact recall 0.74, Jaccard 0.61, 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. 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 Medium
Ames Clear
DILI Risk
Molecular report
Weak
Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-0.706 kcal/mol/HA)
✓ Good fit quality (FQ -6.73)
✓ Deep burial (99% SASA buried)
✓ Lipophilic contacts well-matched (72%)
✗ Very high strain energy (38.7 kcal/mol)
✗ Geometry warnings
✗ Minor protein-contact clashes (2)
✗ Internal clashes (9)
Score
-20.459
kcal/mol
LE
-0.706
kcal/mol/HA
Fit Quality
-6.73
FQ (Leeson)
HAC
29
heavy atoms
MW
428
Da
LogP
4.13
cLogP
Final rank
0.3839
rank score
Inter norm
-1.077
normalised
Contacts
18
H-bonds 3
Interaction summary
HBA 2
HY 10
PI 3
CLASH 2
Interaction summary
HBA 2
HY 10
PI 3
CLASH 2
HBD/HBA · H-bonds (geometric)
HBD = ligand donates H · HBA = ligand accepts H · ~ = weak (≥110°). Mode: permissive. Residues: 2.
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 | TbPTR1_cW_6RX6_Ready | Contacts | 19 |
|---|---|---|---|
| Pose | Open native pose | HB | 0 |
| IFP residues |
ARG14
ASP161
CYS168
GLY205
LEU208
LEU209
LYS178
MET213
NAP301
PHE171
PHE97
PRO210
PRO99
SER207
SER95
TRP221
TYR174
TYR98
VAL206
| ||
| Current overlap | 14 | Native recall | 0.74 |
| Jaccard | 0.61 | RMSD | - |
| HB strict | 0 | Strict recall | 0.00 |
| HB same residue+role | 0 | HB role recall | 0.00 |
| HB same residue | 1 | HB residue recall | 0.20 |
Protein summary
275 residues
| Protein target | T07 | Atoms | 3932 |
|---|---|---|---|
| Residues | 275 | Chains | 3 |
| Residue summary | LEU:437; VAL:433; ALA:361; ARG:288; ILE:266; GLU:210; LYS:198; SER:198; ASN:182; THR:154; GLN:153; PHE:140; PRO:140; TYR:126; GLY:112; HIS:103 | ||
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:NAP301
All stored poses for this docking hit
| Pose | Final rank | Inter norm | Score | HB | CT | CT overlap | CT recall | HB role rec. | RMSD | Excluded | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 120 | 0.3838975461445835 | -1.07679 | -20.459 | 3 | 18 | 14 | 0.74 | 0.00 | - | no | Current |
| 500 | 2.370187323226859 | -0.88212 | -23.2884 | 7 | 13 | 0 | 0.00 | 0.00 | - | no | Open |
| 118 | 2.6329449815392847 | -0.910811 | -24.5174 | 2 | 17 | 0 | 0.00 | 0.00 | - | no | Open |
| 90 | 3.3287066334218705 | -0.964269 | -23.5227 | 7 | 20 | 0 | 0.00 | 0.00 | - | no | Open |
| 506 | 3.3404529615462035 | -0.952543 | -23.435 | 8 | 20 | 0 | 0.00 | 0.00 | - | no | Open |
| 504 | 3.3802376458528895 | -0.933988 | -24.0864 | 11 | 14 | 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
-20.459kcal/mol
Ligand efficiency (LE)
-0.7055kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-6.734
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
29HA
Physicochemical properties
Molecular weight
427.5Da
Lipinski: ≤ 500 Da
LogP (cLogP)
4.13
Lipinski: ≤ 5
Rotatable bonds
6
Conformational strain (MMFF94s)
Strain energy (ΔE)
38.68kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
84.29kcal/mol
Minimised FF energy
45.61kcal/mol
SASA & burial
✓ computed
SASA (unbound)
659.8Ų
Total solvent-accessible surface area of free ligand
BSA total
653.0Ų
Buried surface area upon binding
BSA apolar
471.6Ų
Hydrophobic contacts buried
BSA polar
181.5Ų
Polar contacts buried
Fraction buried
99.0%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
72.2%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-1613.9Ų
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
2051.9Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA
916.3Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)