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
Weak or marginal quality
Binding strong
Geometry high
Native strong
SASA done
Strain ΔE
25.6 kcal/mol
Protein clashes
1
Internal clashes
2
Native overlap
contact recall 0.53, Jaccard 0.45, H-bond role recall 0.80
Reason: no major geometry red flags detected
1 protein-contact clashes
61% of hydrophobic surface is solvent-exposed (11/18 atoms). Large non-polar area without protein contacts incurs a desolvation penalty and will reduce binding affinity. Consider truncating or replacing the exposed fragment.
EcoTox / ADMET
In-silico prediction only
Fish LC₅₀
Not classified (>100 mg/L)
Daphnia EC₅₀
Not classified (>100 mg/L)
Algae IC₅₀
Not classified (>100 mg/L)
Bioaccum.
Not B (BCF≤2000)
Persistent
No
ADMET alerts (in-silico)
hERG Low
Ames Clear
DILI Low
Molecular report
Weak
Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-1.149 kcal/mol/HA)
✓ Good fit quality (FQ -10.58)
✓ Strong H-bond network (6 bonds)
✓ Deep burial (79% SASA buried)
✓ Lipophilic contacts well-matched (61%)
✗ High strain energy (25.6 kcal/mol)
✗ Geometry warnings
✗ Internal clashes (9)
Score
-29.867
kcal/mol
LE
-1.149
kcal/mol/HA
Fit Quality
-10.58
FQ (Leeson)
HAC
26
heavy atoms
MW
362
Da
LogP
1.68
cLogP
Final rank
2.5839
rank score
Inter norm
-1.263
normalised
Contacts
13
H-bonds 13
Interaction summary
HBD 2
HBA 4
HY 2
PI 1
CLASH 2
Interaction summary
HBD 2
HBA 4
HY 2
PI 1
CLASH 2
HBD/HBA · H-bonds (geometric)
HBD = ligand donates H · HBA = ligand accepts H · ~ = weak (≥110°). Mode: permissive. Residues: 5.
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 | 10 | Native recall | 0.53 |
| Jaccard | 0.45 | RMSD | - |
| HB strict | 3 | Strict recall | 0.50 |
| HB same residue+role | 4 | HB role recall | 0.80 |
| HB same residue | 4 | HB residue recall | 0.80 |
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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 22 | 2.5838861387704606 | -1.2632 | -29.867 | 13 | 13 | 10 | 0.53 | 0.80 | - | no | Current |
| 4 | 2.70442284656063 | -1.34129 | -30.5375 | 15 | 20 | 0 | 0.00 | 0.00 | - | no | Open |
| 6 | 2.907867000834636 | -1.15827 | -16.6114 | 14 | 22 | 0 | 0.00 | 0.00 | - | no | Open |
| 6 | 3.6448564737975433 | -1.05551 | -17.6369 | 16 | 18 | 0 | 0.00 | 0.00 | - | no | Open |
| 15 | 4.181017864864475 | -0.86664 | -19.3626 | 8 | 11 | 0 | 0.00 | 0.00 | - | no | Open |
| 4 | 4.813112935699173 | -1.0527 | -24.8236 | 15 | 19 | 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
-29.867kcal/mol
Ligand efficiency (LE)
-1.1487kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-10.584
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
26HA
Physicochemical properties
Molecular weight
362.3Da
Lipinski: ≤ 500 Da
LogP (cLogP)
1.68
Lipinski: ≤ 5
Rotatable bonds
11
Conformational strain (MMFF94s)
Strain energy (ΔE)
25.62kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
55.31kcal/mol
Minimised FF energy
29.69kcal/mol
SASA & burial
✓ computed
SASA (unbound)
622.0Ų
Total solvent-accessible surface area of free ligand
BSA total
493.2Ų
Buried surface area upon binding
BSA apolar
299.9Ų
Hydrophobic contacts buried
BSA polar
193.3Ų
Polar contacts buried
Fraction buried
79.3%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
60.8%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-1512.6Ų
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
962.0Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)