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
14.5 kcal/mol
Protein clashes
1
Internal clashes
2
Native overlap
contact recall 0.74, Jaccard 0.74, H-bond role recall 0.40
Reason: no major geometry red flags detected
1 protein-contact clashes
Molecular report
Promising
Reasonable quality metrics. Warrants further investigation.
✓ Excellent LE (-1.214 kcal/mol/HA)
✓ Good fit quality (FQ -11.32)
✓ Good H-bonds (4 bonds)
✓ Deep burial (86% SASA buried)
✓ Lipophilic contacts well-matched (80%)
✗ Moderate strain (14.5 kcal/mol)
✗ Geometry warnings
✗ Minor protein-contact clashes (4)
✗ Internal clashes (8)
Score
-32.773
kcal/mol
LE
-1.214
kcal/mol/HA
Fit Quality
-11.32
FQ (Leeson)
HAC
27
heavy atoms
MW
424
Da
LogP
3.53
cLogP
Interaction summary
HB 4
HY 24
PI 3
CLASH 2
Interaction summary
HB 4
HY 24
PI 3
CLASH 2
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 | 0.481 | Score | -32.773 |
|---|---|---|---|
| Inter norm | -1.184 | Intra norm | -0.029 |
| Top1000 | no | Excluded | no |
| Contacts | 14 | H-bonds | 4 |
| Artifact reason | geometry warning; 8 clashes; 4 protein contact clashes; 1 cofactor-context clash | ||
| Residues |
ARG14
ASP161
CYS168
GLY205
LEU208
LEU209
LYS178
MET213
NAP301
PHE97
PRO210
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 | 14 | Native recall | 0.74 |
| Jaccard | 0.74 | RMSD | - |
| HB strict | 2 | Strict recall | 0.33 |
| 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 658 | 0.17747997578794278 | -0.940083 | -23.7996 | 0 | 13 | 0 | 0.00 | 0.00 | - | no | Open |
| 653 | 0.3854183286431568 | -1.00593 | -28.2417 | 2 | 14 | 0 | 0.00 | 0.00 | - | no | Open |
| 651 | 0.48112267561454103 | -1.18435 | -32.7731 | 4 | 14 | 14 | 0.74 | 0.40 | - | no | Current |
| 655 | 1.6488674995043928 | -0.903075 | -24.4267 | 5 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 641 | 2.1844053499869824 | -0.963373 | -25.9881 | 3 | 18 | 0 | 0.00 | 0.00 | - | no | Open |
| 659 | 2.474532204339432 | -0.978878 | -26.1669 | 3 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 671 | 2.9208509696607923 | -1.17207 | -31.5025 | 10 | 25 | 0 | 0.00 | 0.00 | - | no | Open |
| 653 | 3.6707947545783903 | -1.06642 | -28.3122 | 8 | 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
-32.773kcal/mol
Ligand efficiency (LE)
-1.2138kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-11.324
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
27HA
Physicochemical properties
Molecular weight
423.9Da
Lipinski: ≤ 500 Da
LogP (cLogP)
3.53
Lipinski: ≤ 5
Rotatable bonds
5
Conformational strain (MMFF94s)
Strain energy (ΔE)
14.55kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
-2.03kcal/mol
Minimised FF energy
-16.57kcal/mol
SASA & burial
✓ computed
SASA (unbound)
642.3Ų
Total solvent-accessible surface area of free ligand
BSA total
552.8Ų
Buried surface area upon binding
BSA apolar
439.4Ų
Hydrophobic contacts buried
BSA polar
113.4Ų
Polar contacts buried
Fraction buried
86.1%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
79.5%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-1648.2Ų
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
915.1Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)