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 but geometrically suspicious
Binding strong
Geometry low
Native strong
SASA done
Strain ΔE
19.4 kcal/mol
Protein clashes
3
Internal clashes
7
Native overlap
contact recall 0.93, Jaccard 0.76, H-bond role recall 0.33
Reason: 7 internal clashes
3 protein-contact clashes
7 intramolecular clashes
48% of hydrophobic surface appears solvent-exposed (14/29 atoms). Partial exposure is common but may limit selectivity and membrane permeability.
Molecular report
Promising
Reasonable quality metrics. Warrants further investigation.
✓ Excellent LE (-0.807 kcal/mol/HA)
✓ Good fit quality (FQ -7.78)
✓ Good H-bonds (5 bonds)
✓ Deep burial (73% SASA buried)
✓ Lipophilic contacts well-matched (95%)
✗ Moderate strain (19.4 kcal/mol)
✗ Geometry warnings
✗ Minor protein-contact clashes (3)
✗ Internal clashes (7)
Score
-24.209
kcal/mol
LE
-0.807
kcal/mol/HA
Fit Quality
-7.78
FQ (Leeson)
HAC
30
heavy atoms
MW
415
Da
LogP
8.02
cLogP
Interaction summary
HB 5
HY 9
PI 0
CLASH 0
⚠ Exposure 48%
Interaction summary
HB 5
HY 9
PI 0
CLASH 0
⚠ Exposure 48%
HB · H-bonds
Mode: strict. Count shows atom-level H-bonds; unique residues in summary: 0.
PI · π–π interactions
No pi · π–π interactions detected for this pose.
HY · Hydrophobic contacts
CLASH · Clashes
No clash · clashes detected for this pose.
Partial hydrophobic solvent exposure
48% of hydrophobic surface appears solvent-exposed (14/29 atoms). Partial exposure is common but may limit selectivity and membrane permeability.
Non-polar atoms 29
Buried (contacted) 15
Exposed 14
LogP 8.02
H-bonds 5
Exposed fragments:
cyclohexyl (2/6 atoms exposed)aliphatic chain/group (12 atoms exposed)
| Final rank | 0.593 | Score | -24.209 |
|---|---|---|---|
| Inter norm | -0.805 | Intra norm | -0.002 |
| Top1000 | no | Excluded | no |
| Contacts | 16 | H-bonds | 5 |
| Artifact reason | geometry warning; 7 clashes; 3 protein contact clashes | ||
| Residues |
ARG137
ARG141
ASN103
HIS102
ARG113
ASP10
CYS69
GLY70
GLY72
GLY74
HIS11
ILE73
PRO12
SER43
SER71
TYR46
| ||
Native ligand reference
★ reference
Interaction fingerprint calculated directly from the uploaded native ligand without docking. Current H-bond mode: strict.
| Name | 3K7O | Contacts | 14 |
|---|---|---|---|
| Pose | Open native pose | HB | 0 |
| IFP residues |
ARG137
ARG141
ASN103
HIS102
HIS138
ASP10
CYS69
GLY70
GLY74
HIS11
ILE73
PRO12
SER71
TYR46
| ||
| Current overlap | 13 | Native recall | 0.93 |
| Jaccard | 0.76 | RMSD | - |
| HB strict | 3 | Strict recall | 0.25 |
| HB same residue+role | 3 | HB role recall | 0.33 |
| HB same residue | 4 | HB residue recall | 0.50 |
Protein summary
305 residues
| Protein target | T21 | Atoms | 4646 |
|---|---|---|---|
| Residues | 305 | Chains | 2 |
| Residue summary | ARG:576; ILE:532; VAL:512; GLU:420; ALA:360; PHE:240; HIS:238; LYS:220; THR:210; LEU:190; PRO:168; TYR:168; GLY:154; SER:154; ASP:144; ASN:112 | ||
All stored poses for this docking hit
| Pose | Final rank | Inter norm | Score | HB | CT | CT overlap | CT recall | HB role rec. | RMSD | Excluded | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 56 | 0.5931377942177519 | -0.805461 | -24.2093 | 5 | 16 | 13 | 0.93 | 0.33 | - | no | Current |
Molecular metrics
RDKit SASA burial, strain energy (MMFF94s), ligand efficiency and fit quality for this docking pose.
Scoring & efficiency
Docking score
-24.209kcal/mol
Ligand efficiency (LE)
-0.8070kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-7.784
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
30HA
Physicochemical properties
Molecular weight
414.7Da
Lipinski: ≤ 500 Da
LogP (cLogP)
8.02
Lipinski: ≤ 5
Rotatable bonds
7
Conformational strain (MMFF94s)
Strain energy (ΔE)
19.43kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
86.89kcal/mol
Minimised FF energy
67.46kcal/mol
SASA & burial
✓ computed
SASA (unbound)
707.8Ų
Total solvent-accessible surface area of free ligand
BSA total
516.2Ų
Buried surface area upon binding
BSA apolar
488.6Ų
Hydrophobic contacts buried
BSA polar
27.6Ų
Polar contacts buried
Fraction buried
72.9%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
94.7%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-2417.8Ų
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
2482.0Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA
744.4Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)