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
14.5 kcal/mol
Protein clashes
3
Internal clashes
8
Native overlap
contact recall 0.93, Jaccard 0.76, H-bond role recall 0.33
Reason: 8 internal clashes
3 protein-contact clashes
8 intramolecular clashes
37% of hydrophobic surface appears solvent-exposed (10/27 atoms). Partial exposure is common but may limit selectivity and membrane permeability.
Molecular report
Promising
Reasonable quality metrics. Warrants further investigation.
✓ Excellent LE (-0.851 kcal/mol/HA)
✓ Good fit quality (FQ -8.03)
✓ Good H-bonds (5 bonds)
✓ Deep burial (76% SASA buried)
✓ Lipophilic contacts well-matched (95%)
✗ Moderate strain (14.5 kcal/mol)
✗ Geometry warnings
✗ Minor protein-contact clashes (3)
✗ Internal clashes (8)
Score
-23.823
kcal/mol
LE
-0.851
kcal/mol/HA
Fit Quality
-8.03
FQ (Leeson)
HAC
28
heavy atoms
MW
381
Da
LogP
7.00
cLogP
Interaction summary
HB 5
HY 13
PI 0
CLASH 0
⚠ Exposure 37%
Interaction summary
HB 5
HY 13
PI 0
CLASH 0
⚠ Exposure 37%
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
37% of hydrophobic surface appears solvent-exposed (10/27 atoms). Partial exposure is common but may limit selectivity and membrane permeability.
Non-polar atoms 27
Buried (contacted) 17
Exposed 10
LogP 7.0
H-bonds 5
Exposed fragments:
aliphatic chain/group (10 atoms exposed)
| Final rank | 0.481 | Score | -23.823 |
|---|---|---|---|
| Inter norm | -0.972 | Intra norm | 0.121 |
| Top1000 | no | Excluded | no |
| Contacts | 16 | H-bonds | 5 |
| Artifact reason | geometry warning; 8 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 48 | 0.4808386885853659 | -0.97173 | -23.8233 | 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
-23.823kcal/mol
Ligand efficiency (LE)
-0.8508kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-8.032
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
28HA
Physicochemical properties
Molecular weight
380.6Da
Lipinski: ≤ 500 Da
LogP (cLogP)
7.00
Lipinski: ≤ 5
Rotatable bonds
4
Conformational strain (MMFF94s)
Strain energy (ΔE)
14.52kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
78.57kcal/mol
Minimised FF energy
64.05kcal/mol
SASA & burial
✓ computed
SASA (unbound)
664.5Ų
Total solvent-accessible surface area of free ligand
BSA total
506.9Ų
Buried surface area upon binding
BSA apolar
479.7Ų
Hydrophobic contacts buried
BSA polar
27.2Ų
Polar contacts buried
Fraction buried
76.3%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
94.6%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-2372.2Ų
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
2482.0Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA
747.1Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)