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
39.3 kcal/mol
Protein clashes
0
Internal clashes
1
Native overlap
contact recall 0.63, Jaccard 0.63, H-bond role recall 0.40
Reason: no major geometry red flags detected
44% of hydrophobic surface appears solvent-exposed (4/9 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 (-1.361 kcal/mol/HA)
✓ Good fit quality (FQ -10.90)
✓ Good H-bonds (5 bonds)
✓ Deep burial (97% SASA buried)
✓ Lipophilic contacts well-matched (71%)
✗ Very high strain energy (39.3 kcal/mol)
✗ Geometry warnings
✗ Internal clashes (5)
Score
-24.491
kcal/mol
LE
-1.361
kcal/mol/HA
Fit Quality
-10.90
FQ (Leeson)
HAC
18
heavy atoms
MW
275
Da
LogP
-1.47
cLogP
Final rank
0.6956
rank score
Inter norm
-1.672
normalised
Contacts
12
H-bonds 10
Interaction summary
HBD 4
HBA 1
HY 4
PI 2
CLASH 1
Interaction summary
HBD 4
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: 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: 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 | 12 | Native recall | 0.63 |
| Jaccard | 0.63 | 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
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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 91 | -0.08226211654963808 | -1.39346 | -20.1278 | 7 | 13 | 0 | 0.00 | 0.00 | - | no | Open |
| 154 | 0.6955724036698013 | -1.6722 | -24.4909 | 10 | 12 | 12 | 0.63 | 0.40 | - | no | Current |
| 135 | 2.859399509952881 | -1.53959 | -26.1699 | 16 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 111 | 3.868195778633708 | -1.33478 | -19.7233 | 14 | 16 | 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
-24.491kcal/mol
Ligand efficiency (LE)
-1.3606kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-10.904
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
18HA
Physicochemical properties
Molecular weight
274.7Da
Lipinski: ≤ 500 Da
LogP (cLogP)
-1.47
Lipinski: ≤ 5
Rotatable bonds
8
Conformational strain (MMFF94s)
Strain energy (ΔE)
39.32kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
105.11kcal/mol
Minimised FF energy
65.80kcal/mol
SASA & burial
✓ computed
SASA (unbound)
449.1Ų
Total solvent-accessible surface area of free ligand
BSA total
434.8Ų
Buried surface area upon binding
BSA apolar
309.4Ų
Hydrophobic contacts buried
BSA polar
125.4Ų
Polar contacts buried
Fraction buried
96.8%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
71.2%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-1447.5Ų
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
924.0Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)