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 strong
SASA done
Strain ΔE
18.2 kcal/mol
Protein clashes
4
Internal clashes
4
Native overlap
contact recall 0.68, Jaccard 0.54, H-bond role recall 0.60
Reason: no major geometry red flags detected
4 protein-contact clashes
4 intramolecular 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 Medium
Ames Clear
DILI Low
Molecular report
Promising
Reasonable quality metrics. Warrants further investigation.
✓ Excellent LE (-1.174 kcal/mol/HA)
✓ Good fit quality (FQ -10.82)
✓ Good H-bonds (3 bonds)
✓ Deep burial (99% SASA buried)
✓ Lipophilic contacts well-matched (86%)
✗ Moderate strain (18.2 kcal/mol)
✗ Geometry warnings
✗ Internal clashes (7)
Score
-30.528
kcal/mol
LE
-1.174
kcal/mol/HA
Fit Quality
-10.82
FQ (Leeson)
HAC
26
heavy atoms
MW
346
Da
LogP
2.92
cLogP
Final rank
2.8643
rank score
Inter norm
-1.202
normalised
Contacts
18
H-bonds 6
Interaction summary
HBD 2
HBA 1
HY 9
PI 4
CLASH 4
Interaction summary
HBD 2
HBA 1
HY 9
PI 4
CLASH 4
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 | 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 | 13 | Native recall | 0.68 |
| Jaccard | 0.54 | RMSD | - |
| HB strict | 2 | Strict recall | 0.33 |
| HB same residue+role | 3 | HB role recall | 0.60 |
| HB same residue | 4 | HB residue recall | 0.80 |
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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 157 | 0.7117618756533478 | -1.00994 | -20.113 | 3 | 20 | 0 | 0.00 | 0.00 | - | no | Open |
| 87 | 2.2585325691088283 | -1.09229 | -25.7372 | 7 | 21 | 0 | 0.00 | 0.00 | - | no | Open |
| 149 | 2.513102290808282 | -1.2589 | -32.4954 | 6 | 18 | 13 | 0.68 | 0.60 | - | no | Open |
| 110 | 2.864260999450896 | -1.20208 | -30.5278 | 6 | 18 | 13 | 0.68 | 0.60 | - | no | Current |
| 129 | 3.1430621533001446 | -0.817155 | -20.782 | 5 | 13 | 0 | 0.00 | 0.00 | - | no | Open |
| 108 | 3.414687968297742 | -1.21617 | -27.759 | 10 | 18 | 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
-30.528kcal/mol
Ligand efficiency (LE)
-1.1741kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-10.818
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
26HA
Physicochemical properties
Molecular weight
346.4Da
Lipinski: ≤ 500 Da
LogP (cLogP)
2.92
Lipinski: ≤ 5
Rotatable bonds
4
Conformational strain (MMFF94s)
Strain energy (ΔE)
18.24kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
60.85kcal/mol
Minimised FF energy
42.61kcal/mol
SASA & burial
✓ computed
SASA (unbound)
624.7Ų
Total solvent-accessible surface area of free ligand
BSA total
619.1Ų
Buried surface area upon binding
BSA apolar
529.7Ų
Hydrophobic contacts buried
BSA polar
89.4Ų
Polar contacts buried
Fraction buried
99.1%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
85.6%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-1666.7Ų
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
918.2Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)