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 medium
Native strong
SASA done
Strain ΔE
19.6 kcal/mol
Protein clashes
2
Internal clashes
4
Native overlap
contact recall 0.63, Jaccard 0.55, H-bond role recall 0.40
Reason: no major geometry red flags detected
2 protein-contact clashes
4 intramolecular clashes
36% of hydrophobic surface appears solvent-exposed (9/25 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 (-1.081 kcal/mol/HA)
✓ Good fit quality (FQ -10.53)
✓ Deep burial (84% SASA buried)
✓ Lipophilic contacts well-matched (88%)
✗ Moderate strain (19.6 kcal/mol)
✗ Geometry warnings
✗ Minor protein-contact clashes (2)
✗ Many internal clashes (16)
Score
-33.515
kcal/mol
LE
-1.081
kcal/mol/HA
Fit Quality
-10.53
FQ (Leeson)
HAC
31
heavy atoms
MW
416
Da
LogP
2.55
cLogP
Final rank
1.0230
rank score
Inter norm
-1.099
normalised
Contacts
15
H-bonds 5
Interaction summary
HBD 2
HY 8
PI 4
CLASH 4
Interaction summary
HBD 2
HY 8
PI 4
CLASH 4
HBD/HBA · H-bonds (geometric)
HBD = ligand donates H · HBA = ligand accepts H · ~ = weak (≥110°). Mode: permissive. Residues: 1.
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 | 12 | Native recall | 0.63 |
| Jaccard | 0.55 | RMSD | - |
| HB strict | 1 | Strict recall | 0.17 |
| 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 199 | 1.0229683979393438 | -1.09948 | -33.5151 | 5 | 15 | 12 | 0.63 | 0.40 | - | no | Current |
| 229 | 1.1269332158851013 | -1.1119 | -33.699 | 5 | 15 | 13 | 0.68 | 0.40 | - | no | Open |
| 203 | 2.634996494585596 | -0.771533 | -21.5507 | 4 | 18 | 0 | 0.00 | 0.00 | - | no | Open |
| 183 | 2.874014784843524 | -0.772555 | -21.5943 | 4 | 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
-33.515kcal/mol
Ligand efficiency (LE)
-1.0811kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-10.533
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
31HA
Physicochemical properties
Molecular weight
415.5Da
Lipinski: ≤ 500 Da
LogP (cLogP)
2.55
Lipinski: ≤ 5
Rotatable bonds
5
Conformational strain (MMFF94s)
Strain energy (ΔE)
19.58kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
9.78kcal/mol
Minimised FF energy
-9.80kcal/mol
SASA & burial
✓ computed
SASA (unbound)
723.0Ų
Total solvent-accessible surface area of free ligand
BSA total
610.7Ų
Buried surface area upon binding
BSA apolar
539.4Ų
Hydrophobic contacts buried
BSA polar
71.3Ų
Polar contacts buried
Fraction buried
84.5%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
88.3%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-1780.9Ų
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
922.7Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)