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
8.3 kcal/mol
Protein clashes
3
Internal clashes
2
Native overlap
contact recall 0.68, Jaccard 0.62, H-bond role recall 0.60
Reason: no major geometry red flags detected
3 protein-contact clashes
Molecular report
Promising
Reasonable quality metrics. Warrants further investigation.
✓ Excellent LE (-1.642 kcal/mol/HA)
✓ Good fit quality (FQ -14.01)
✓ Strong H-bond network (9 bonds)
✓ Deep burial (97% SASA buried)
✓ Lipophilic contacts well-matched (66%)
✗ Moderate strain (8.3 kcal/mol)
✗ Geometry warnings
✗ Minor protein-contact clashes (3)
✗ Internal clashes (8)
Score
-34.486
kcal/mol
LE
-1.642
kcal/mol/HA
Fit Quality
-14.01
FQ (Leeson)
HAC
21
heavy atoms
MW
286
Da
LogP
1.09
cLogP
Interaction summary
HB 9
HY 24
PI 1
CLASH 2
Interaction summary
HB 9
HY 24
PI 1
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 | -0.188 | Score | -34.486 |
|---|---|---|---|
| Inter norm | -1.674 | Intra norm | 0.032 |
| Top1000 | no | Excluded | no |
| Contacts | 15 | H-bonds | 9 |
| Artifact reason | geometry warning; 8 clashes; 3 protein contact clashes; 2 severe cofactor-context clashes | ||
| Residues |
ARG14
ASP161
CYS168
LEU208
LEU209
LEU263
LYS178
MET163
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 | 13 | Native recall | 0.68 |
| Jaccard | 0.62 | 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 75 | -0.18772052928976135 | -1.67402 | -34.4856 | 9 | 15 | 13 | 0.68 | 0.60 | - | no | Current |
| 87 | 1.0348770914528322 | -1.69392 | -30.7065 | 8 | 14 | 12 | 0.63 | 0.40 | - | no | Open |
| 57 | 1.627289209155493 | -1.37907 | -27.2207 | 7 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 45 | 2.59172040695213 | -1.24871 | -24.0985 | 5 | 10 | 0 | 0.00 | 0.00 | - | no | Open |
| 67 | 3.8837927447896012 | -1.2417 | -24.3403 | 9 | 13 | 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
-34.486kcal/mol
Ligand efficiency (LE)
-1.6422kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-14.007
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
21HA
Physicochemical properties
Molecular weight
286.2Da
Lipinski: ≤ 500 Da
LogP (cLogP)
1.09
Lipinski: ≤ 5
Rotatable bonds
4
Conformational strain (MMFF94s)
Strain energy (ΔE)
8.28kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
59.08kcal/mol
Minimised FF energy
50.80kcal/mol
SASA & burial
✓ computed
SASA (unbound)
485.8Ų
Total solvent-accessible surface area of free ligand
BSA total
470.8Ų
Buried surface area upon binding
BSA apolar
311.7Ų
Hydrophobic contacts buried
BSA polar
159.1Ų
Polar contacts buried
Fraction buried
96.9%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
66.2%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-1456.9Ų
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
915.8Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)