Molecular metrics status: done
RDKit SASA-based burial metrics are cached.
SASA cached
3D complex viewer
Viewer legend
Protein receptor
Pocket residues
Cofactor context
Docked ligand
Overall assessment
Promising
SASA cached
Promising and worth follow-up
Binding strong
Geometry high
Native strong
SASA done
Strain ΔE
17.1 kcal/mol
Protein clashes
1
Internal clashes
1
Native overlap
contact recall 0.63, Jaccard 0.57, H-bond role recall 0.60
Reason: no major geometry red flags detected
1 protein-contact clashes
Molecular report
Promising
Reasonable quality metrics. Warrants further investigation.
✓ Excellent LE (-1.652 kcal/mol/HA)
✓ Good fit quality (FQ -12.92)
✓ Strong H-bond network (6 bonds)
✓ Deep burial (97% SASA buried)
✓ Lipophilic contacts well-matched (76%)
✗ Moderate strain (17.1 kcal/mol)
✗ Geometry warnings
✗ Minor protein-contact clashes (2)
✗ Internal clashes (5)
Score
-28.086
kcal/mol
LE
-1.652
kcal/mol/HA
Fit Quality
-12.92
FQ (Leeson)
HAC
17
heavy atoms
MW
235
Da
LogP
-0.33
cLogP
Interaction summary
HB 6
HY 13
PI 3
CLASH 1
Interaction summary
HB 6
HY 13
PI 3
CLASH 1
HB · H-bonds
Mode: strict. Count shows atom-level H-bonds; unique residues in summary: 0.
PI · π–π interactions
Native π–π recall is disabled because no explicit native π–π reference was stored.
HY · Hydrophobic contacts
CLASH · Clashes
| Final rank | -0.975 | Score | -28.086 |
|---|---|---|---|
| Inter norm | -1.907 | Intra norm | 0.255 |
| Top1000 | no | Excluded | no |
| Contacts | 14 | H-bonds | 6 |
| Artifact reason | geometry warning; 5 clashes; 2 protein contact clashes; 2 cofactor-context clashes | ||
| Residues |
ARG14
GLY205
LEU208
LEU209
LEU263
MET163
MET213
NAP301
PHE97
PRO210
SER95
TRP221
TYR174
VAL206
| ||
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 | 0.57 | 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 223 | -0.9754431735797291 | -1.90731 | -28.0856 | 6 | 14 | 12 | 0.63 | 0.60 | - | no | Current |
| 239 | 0.3591957852715024 | -1.85909 | -27.0217 | 5 | 10 | 0 | 0.00 | 0.00 | - | no | Open |
| 193 | 0.8776894841038055 | -1.65348 | -23.9391 | 9 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 267 | 1.8122154727434479 | -1.715 | -26.7391 | 9 | 11 | 0 | 0.00 | 0.00 | - | no | Open |
| 199 | 3.3999241799255477 | -1.85546 | -29.6982 | 13 | 17 | 0 | 0.00 | 0.00 | - | no | Open |
| 270 | 3.545440099450609 | -1.12148 | -17.6237 | 6 | 9 | 0 | 0.00 | 0.00 | - | no | Open |
| 248 | 3.607817294976168 | -1.32219 | -24.4615 | 9 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 355 | 4.0808226831180825 | -1.49117 | -23.0442 | 7 | 12 | 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
-28.086kcal/mol
Ligand efficiency (LE)
-1.6521kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-12.919
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
17HA
Physicochemical properties
Molecular weight
235.3Da
Lipinski: ≤ 500 Da
LogP (cLogP)
-0.33
Lipinski: ≤ 5
Rotatable bonds
7
Conformational strain (MMFF94s)
Strain energy (ΔE)
17.05kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
11.28kcal/mol
Minimised FF energy
-5.77kcal/mol
SASA & burial
✓ computed
SASA (unbound)
457.0Ų
Total solvent-accessible surface area of free ligand
BSA total
444.8Ų
Buried surface area upon binding
BSA apolar
340.0Ų
Hydrophobic contacts buried
BSA polar
104.7Ų
Polar contacts buried
Fraction buried
97.3%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
76.5%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-1476.2Ų
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
922.4Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)