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
23.1 kcal/mol
Protein clashes
3
Internal clashes
1
Native overlap
contact recall 0.79, Jaccard 0.65, H-bond role recall 0.60
Reason: no major geometry red flags detected
3 protein-contact clashes
35% of hydrophobic surface appears solvent-exposed (7/20 atoms). Partial exposure is common but may limit selectivity and membrane permeability.
Molecular report
Weak
Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-0.930 kcal/mol/HA)
✓ Good fit quality (FQ -9.06)
✓ Good H-bonds (5 bonds)
✓ Deep burial (79% SASA buried)
✓ Lipophilic contacts well-matched (73%)
✗ High strain energy (23.1 kcal/mol)
✗ Geometry warnings
✗ Minor protein-contact clashes (3)
✗ Internal clashes (9)
Score
-28.817
kcal/mol
LE
-0.930
kcal/mol/HA
Fit Quality
-9.06
FQ (Leeson)
HAC
31
heavy atoms
MW
428
Da
LogP
0.50
cLogP
Final rank
0.4528
rank score
Inter norm
-1.130
normalised
Contacts
19
H-bonds 14
Interaction summary
HBD 5
HY 6
PI 5
CLASH 1
Interaction summary
HBD 5
HY 6
PI 5
CLASH 1
HBD/HBA · H-bonds (geometric)
HBD = ligand donates H · HBA = ligand accepts H · ~ = weak (≥110°). Mode: permissive. 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: 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 | 15 | Native recall | 0.79 |
| Jaccard | 0.65 | RMSD | - |
| HB strict | 4 | Strict recall | 0.67 |
| HB same residue+role | 3 | HB role recall | 0.60 |
| HB same residue | 3 | HB residue recall | 0.60 |
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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 461 | 0.45278527588056827 | -1.1302 | -28.8173 | 14 | 19 | 15 | 0.79 | 0.60 | - | no | Current |
| 461 | 2.8485288578572088 | -1.00935 | -22.3742 | 7 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 473 | 3.424763537345141 | -0.942133 | -25.5903 | 15 | 20 | 0 | 0.00 | 0.00 | - | no | Open |
| 523 | 3.9665077067845056 | -0.735459 | -14.2995 | 11 | 24 | 0 | 0.00 | 0.00 | - | no | Open |
| 505 | 4.42474033215533 | -0.995515 | -22.6273 | 9 | 19 | 0 | 0.00 | 0.00 | - | no | Open |
| 476 | 4.438356089261524 | -0.995065 | -23.7009 | 13 | 22 | 0 | 0.00 | 0.00 | - | no | Open |
| 495 | 4.6898011358661975 | -0.724752 | -19.1568 | 9 | 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
-28.817kcal/mol
Ligand efficiency (LE)
-0.9296kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-9.056
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
31HA
Physicochemical properties
Molecular weight
428.4Da
Lipinski: ≤ 500 Da
LogP (cLogP)
0.50
Lipinski: ≤ 5
Rotatable bonds
11
Conformational strain (MMFF94s)
Strain energy (ΔE)
23.06kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
-56.84kcal/mol
Minimised FF energy
-79.90kcal/mol
SASA & burial
✓ computed
SASA (unbound)
720.0Ų
Total solvent-accessible surface area of free ligand
BSA total
571.2Ų
Buried surface area upon binding
BSA apolar
416.7Ų
Hydrophobic contacts buried
BSA polar
154.6Ų
Polar contacts buried
Fraction buried
79.3%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
72.9%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-1626.4Ų
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
911.5Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)