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
Weak
SASA cached
Promising but geometrically suspicious
Binding strong
Geometry low
Native strong
SASA done
Strain ΔE
21.2 kcal/mol
Protein clashes
0
Internal clashes
18
Native overlap
contact recall 0.58, Jaccard 0.52, H-bond role recall 0.40
Reason: 18 internal clashes
18 intramolecular clashes
50% of hydrophobic surface appears solvent-exposed (14/28 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 High
Ames Clear
DILI Risk
Molecular report
Weak
Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-0.789 kcal/mol/HA)
✓ Good fit quality (FQ -8.02)
✓ Good H-bonds (5 bonds)
✓ Deep burial (69% SASA buried)
✓ Lipophilic contacts well-matched (82%)
✗ High strain energy (21.2 kcal/mol)
✗ Geometry warnings
✗ Many internal clashes (18)
Score
-28.410
kcal/mol
LE
-0.789
kcal/mol/HA
Fit Quality
-8.02
FQ (Leeson)
HAC
36
heavy atoms
MW
487
Da
LogP
4.95
cLogP
Final rank
1.2107
rank score
Inter norm
-0.936
normalised
Contacts
13
H-bonds 9
Interaction summary
HBD 4
HBA 1
HY 6
PI 4
CLASH 0
Interaction summary
HBD 4
HBA 1
HY 6
PI 4
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 | 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 | 11 | Native recall | 0.58 |
| Jaccard | 0.52 | RMSD | - |
| HB strict | 2 | Strict recall | 0.33 |
| HB same residue+role | 2 | HB role recall | 0.40 |
| HB same residue | 2 | HB residue recall | 0.40 |
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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 228 | 1.210668734486631 | -0.935701 | -28.41 | 9 | 13 | 11 | 0.58 | 0.40 | - | no | Current |
| 271 | 2.191999564136022 | -0.746465 | -24.0976 | 6 | 12 | 0 | 0.00 | 0.00 | - | no | Open |
| 276 | 2.592891886812236 | -0.705968 | -21.027 | 3 | 18 | 0 | 0.00 | 0.00 | - | no | Open |
| 255 | 2.919592932455517 | -0.678087 | -20.159 | 8 | 22 | 0 | 0.00 | 0.00 | - | no | Open |
| 207 | 5.688113683789827 | -0.904873 | -28.946 | 16 | 25 | 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
-28.410kcal/mol
Ligand efficiency (LE)
-0.7892kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-8.021
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
36HA
Physicochemical properties
Molecular weight
486.6Da
Lipinski: ≤ 500 Da
LogP (cLogP)
4.95
Lipinski: ≤ 5
Rotatable bonds
8
Conformational strain (MMFF94s)
Strain energy (ΔE)
21.17kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
140.42kcal/mol
Minimised FF energy
119.25kcal/mol
SASA & burial
✓ computed
SASA (unbound)
799.4Ų
Total solvent-accessible surface area of free ligand
BSA total
554.5Ų
Buried surface area upon binding
BSA apolar
453.6Ų
Hydrophobic contacts buried
BSA polar
100.9Ų
Polar contacts buried
Fraction buried
69.4%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
81.8%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-1760.9Ų
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
949.1Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)