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 high
Native mixed
SASA done
Strain ΔE
16.5 kcal/mol
Protein clashes
0
Internal clashes
1
Native overlap
contact recall 0.37, Jaccard 0.33, H-bond role recall 0.40
Reason: no major geometry red flags detected
EcoTox / ADMET
In-silico prediction only
Fish LC₅₀
Cat. 2 — Toxic (1–10 mg/L)
Daphnia EC₅₀
Cat. 1 — Very toxic (≤1 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 Low
Molecular report
Promising
Reasonable quality metrics. Warrants further investigation.
✓ Excellent LE (-1.338 kcal/mol/HA)
✓ Good fit quality (FQ -11.81)
✓ Good H-bonds (3 bonds)
✓ Deep burial (85% SASA buried)
✓ Lipophilic contacts well-matched (93%)
✗ Moderate strain (16.5 kcal/mol)
✗ Geometry warnings
✗ Internal clashes (9)
Score
-30.771
kcal/mol
LE
-1.338
kcal/mol/HA
Fit Quality
-11.81
FQ (Leeson)
HAC
23
heavy atoms
MW
305
Da
LogP
4.52
cLogP
Final rank
1.0629
rank score
Inter norm
-1.505
normalised
Contacts
9
H-bonds 8
Interaction summary
HBD 2
HBA 1
HY 4
PI 2
CLASH 1
Interaction summary
HBD 2
HBA 1
HY 4
PI 2
CLASH 1
HBD/HBA · H-bonds (geometric)
HBD = ligand donates H · HBA = ligand accepts H · ~ = weak (≥110°). Mode: strict. 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: 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 | 7 | Native recall | 0.37 |
| Jaccard | 0.33 | RMSD | - |
| HB strict | 3 | Strict recall | 0.50 |
| HB same residue+role | 2 | HB role recall | 0.40 |
| HB same residue | 2 | HB residue recall | 0.40 |
Protein summary
258 residues
| Protein target | T08 | Atoms | 3881 |
|---|---|---|---|
| Residues | 258 | Chains | 2 |
| 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 428 | 0.1950391297033565 | -1.38991 | -30.8293 | 3 | 17 | 13 | 0.68 | 0.00 | - | no | Open |
| 455 | 1.062913512785606 | -1.50491 | -30.7706 | 8 | 9 | 7 | 0.37 | 0.40 | - | no | Current |
| 438 | 3.3679033600549193 | -1.03318 | -22.8315 | 7 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 440 | 3.5654522027493063 | -1.21323 | -21.6344 | 8 | 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
-30.771kcal/mol
Ligand efficiency (LE)
-1.3379kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-11.808
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
23HA
Physicochemical properties
Molecular weight
305.4Da
Lipinski: ≤ 500 Da
LogP (cLogP)
4.52
Lipinski: ≤ 5
Rotatable bonds
3
Conformational strain (MMFF94s)
Strain energy (ΔE)
16.54kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
18.54kcal/mol
Minimised FF energy
2.00kcal/mol
SASA & burial
✓ computed
SASA (unbound)
593.6Ų
Total solvent-accessible surface area of free ligand
BSA total
503.4Ų
Buried surface area upon binding
BSA apolar
466.9Ų
Hydrophobic contacts buried
BSA polar
36.5Ų
Polar contacts buried
Fraction buried
84.8%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
92.7%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-1648.6Ų
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
952.4Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)