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 medium
Native strong
SASA done
Strain ΔE
18.9 kcal/mol
Protein clashes
2
Internal clashes
4
Native overlap
contact recall 0.79, Jaccard 0.62, H-bond role recall 0.40
Reason: no major geometry red flags detected
2 protein-contact clashes
4 intramolecular clashes
Molecular report
Promising
Reasonable quality metrics. Warrants further investigation.
✓ Excellent LE (-1.261 kcal/mol/HA)
✓ Good fit quality (FQ -11.62)
✓ Strong H-bond network (8 bonds)
✓ Deep burial (99% SASA buried)
✓ Lipophilic contacts well-matched (66%)
✗ Moderate strain (18.9 kcal/mol)
✗ Geometry warnings
✗ Internal clashes (9)
Score
-32.778
kcal/mol
LE
-1.261
kcal/mol/HA
Fit Quality
-11.62
FQ (Leeson)
HAC
26
heavy atoms
MW
360
Da
LogP
1.76
cLogP
Interaction summary
HB 8
HY 24
PI 2
CLASH 4
Interaction summary
HB 8
HY 24
PI 2
CLASH 4
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 | 2.516 | Score | -32.778 |
|---|---|---|---|
| Inter norm | -1.291 | Intra norm | 0.030 |
| Top1000 | no | Excluded | no |
| Contacts | 20 | H-bonds | 8 |
| Artifact reason | geometry warning; 9 clashes; 2 protein clashes; 2 severe cofactor-context clashes | ||
| Residues |
ARG14
ASN175
ASP161
CYS168
GLN166
GLY205
LEU208
LEU209
MET163
MET213
NAP301
PHE171
PHE97
PRO167
PRO210
SER95
TRP221
TYR174
VAL164
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 | 15 | Native recall | 0.79 |
| Jaccard | 0.62 | 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
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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 83 | 1.726165603324366 | -1.25521 | -28.9129 | 14 | 11 | 8 | 0.42 | 0.80 | - | no | Open |
| 72 | 2.5159025534805233 | -1.29084 | -32.7784 | 8 | 20 | 15 | 0.79 | 0.40 | - | no | Current |
| 47 | 3.0866835948633713 | -1.21083 | -30.5389 | 12 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 30 | 4.249683644980609 | -0.998616 | -15.5397 | 12 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 65 | 4.3394777699327225 | -1.03572 | -23.6814 | 9 | 19 | 0 | 0.00 | 0.00 | - | no | Open |
| 79 | 4.411040433023151 | -0.928097 | -19.2409 | 8 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 82 | 4.435254214047893 | -0.905021 | -18.9062 | 11 | 13 | 0 | 0.00 | 0.00 | - | no | Open |
| 50 | 5.831249337352885 | -0.940251 | -16.3801 | 15 | 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
-32.778kcal/mol
Ligand efficiency (LE)
-1.2607kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-11.615
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
26HA
Physicochemical properties
Molecular weight
360.3Da
Lipinski: ≤ 500 Da
LogP (cLogP)
1.76
Lipinski: ≤ 5
Rotatable bonds
10
Conformational strain (MMFF94s)
Strain energy (ΔE)
18.86kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
67.61kcal/mol
Minimised FF energy
48.75kcal/mol
SASA & burial
✓ computed
SASA (unbound)
597.2Ų
Total solvent-accessible surface area of free ligand
BSA total
589.3Ų
Buried surface area upon binding
BSA apolar
387.4Ų
Hydrophobic contacts buried
BSA polar
201.9Ų
Polar contacts buried
Fraction buried
98.7%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
65.7%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-1526.9Ų
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
918.0Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)