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
Promising
SASA cached
Promising and worth follow-up
Binding strong
Geometry high
Native strong
SASA done
Strain ΔE
9.3 kcal/mol
Protein clashes
2
Internal clashes
2
Native overlap
contact recall 0.53, Jaccard 0.53, H-bond role recall 0.80
Reason: no major geometry red flags detected
2 protein-contact clashes
Molecular report
Promising
Reasonable quality metrics. Warrants further investigation.
✓ Excellent LE (-2.200 kcal/mol/HA)
✓ Good fit quality (FQ -15.16)
✓ Strong H-bond network (11 bonds)
✓ Deep burial (94% SASA buried)
✓ Lipophilic contacts well-matched (77%)
✗ Moderate strain (9.3 kcal/mol)
✗ Geometry warnings
Score
-28.602
kcal/mol
LE
-2.200
kcal/mol/HA
Fit Quality
-15.16
FQ (Leeson)
HAC
13
heavy atoms
MW
183
Da
LogP
0.35
cLogP
Interaction summary
HB 11
HY 10
PI 1
CLASH 2
Interaction summary
HB 11
HY 10
PI 1
CLASH 2
| Final rank | 0.953 | Score | -28.602 |
|---|---|---|---|
| Inter norm | -2.531 | Intra norm | 0.331 |
| Top1000 | no | Excluded | no |
| Contacts | 10 | H-bonds | 11 |
| Artifact reason | geometry warning; 4 clashes; 2 protein clashes; 1 severe cofactor-context clash | ||
| Residues |
ARG14
ASP161
CYS168
LEU208
LEU209
LYS178
NAP301
PHE97
PRO210
TYR174
| ||
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
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 | 10 | Native recall | 0.53 |
| Jaccard | 0.53 | RMSD | - |
| HB strict | 5 | Strict recall | 0.83 |
| HB same residue+role | 4 | HB role recall | 0.80 |
| HB same residue | 4 | HB residue recall | 0.80 |
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
All stored poses for this docking hit
| Pose | Final rank | Inter norm | Score | HB | CT | CT overlap | CT recall | HB role rec. | RMSD | Excluded | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 607 | 0.9534683220960247 | -2.53145 | -28.6021 | 11 | 10 | 10 | 0.53 | 0.80 | - | no | Current |
| 623 | 1.6082946369248607 | -2.27795 | -23.4845 | 9 | 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
-28.602kcal/mol
Ligand efficiency (LE)
-2.2002kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-15.165
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
13HA
Physicochemical properties
Molecular weight
183.2Da
Lipinski: ≤ 500 Da
LogP (cLogP)
0.35
Lipinski: ≤ 5
Rotatable bonds
6
Conformational strain (MMFF94s)
Strain energy (ΔE)
9.26kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
51.86kcal/mol
Minimised FF energy
42.60kcal/mol
SASA & burial
✓ computed
SASA (unbound)
394.2Ų
Total solvent-accessible surface area of free ligand
BSA total
372.2Ų
Buried surface area upon binding
BSA apolar
286.5Ų
Hydrophobic contacts buried
BSA polar
85.7Ų
Polar contacts buried
Fraction buried
94.4%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
77.0%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-1425.8Ų
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
930.9Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)