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
26.0 kcal/mol
Protein clashes
1
Internal clashes
4
Native overlap
contact recall 0.68, Jaccard 0.68, H-bond role recall 0.60
Reason: no major geometry red flags detected
1 protein-contact clashes
4 intramolecular clashes
40% of hydrophobic surface appears solvent-exposed (4/10 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 (-1.620 kcal/mol/HA)
✓ Good fit quality (FQ -13.56)
✓ Strong H-bond network (6 bonds)
✓ Deep burial (98% SASA buried)
✓ Lipophilic contacts well-matched (66%)
✗ High strain energy (26.0 kcal/mol)
✗ Geometry warnings
✗ Minor protein-contact clashes (4)
✗ Internal clashes (7)
Score
-32.404
kcal/mol
LE
-1.620
kcal/mol/HA
Fit Quality
-13.56
FQ (Leeson)
HAC
20
heavy atoms
MW
305
Da
LogP
-2.11
cLogP
Final rank
-0.0783
rank score
Inter norm
-1.598
normalised
Contacts
13
H-bonds 16
Interaction summary
HBD 4
HBA 2
HY 3
PI 2
CLASH 4
Interaction summary
HBD 4
HBA 2
HY 3
PI 2
CLASH 4
HBD/HBA · H-bonds (geometric)
HBD = ligand donates H · HBA = ligand accepts H · ~ = weak (≥110°). Mode: strict. Residues: 4.
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 | 0.68 | 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 213 | -0.07830540273871364 | -1.59773 | -32.4042 | 16 | 13 | 13 | 0.68 | 0.60 | - | no | Current |
| 228 | 1.1298153099012058 | -1.64897 | -29.6187 | 10 | 11 | 11 | 0.58 | 0.60 | - | no | Open |
| 255 | 3.088123441932323 | -1.4505 | -26.7354 | 11 | 9 | 0 | 0.00 | 0.00 | - | no | Open |
| 153 | 3.260548858977111 | -1.468 | -30.6734 | 11 | 17 | 0 | 0.00 | 0.00 | - | no | Open |
| 173 | 4.765747594874439 | -1.41151 | -23.2273 | 14 | 15 | 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
-32.404kcal/mol
Ligand efficiency (LE)
-1.6202kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-13.558
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
20HA
Physicochemical properties
Molecular weight
304.7Da
Lipinski: ≤ 500 Da
LogP (cLogP)
-2.11
Lipinski: ≤ 5
Rotatable bonds
10
Conformational strain (MMFF94s)
Strain energy (ΔE)
25.96kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
115.36kcal/mol
Minimised FF energy
89.40kcal/mol
SASA & burial
✓ computed
SASA (unbound)
448.3Ų
Total solvent-accessible surface area of free ligand
BSA total
437.9Ų
Buried surface area upon binding
BSA apolar
290.4Ų
Hydrophobic contacts buried
BSA polar
147.5Ų
Polar contacts buried
Fraction buried
97.7%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
66.3%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-1427.6Ų
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
920.2Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)