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
10.1 kcal/mol
Protein clashes
1
Internal clashes
1
Native overlap
contact recall 1.00, Jaccard 0.78, H-bond role recall 0.44
Reason: no major geometry red flags detected
1 protein-contact clashes
Molecular report
Promising
Reasonable quality metrics. Warrants further investigation.
✓ Excellent LE (-1.242 kcal/mol/HA)
✓ Good fit quality (FQ -10.39)
✓ Strong H-bond network (6 bonds)
✓ Deep burial (88% SASA buried)
✓ Lipophilic contacts well-matched (89%)
✗ Moderate strain (10.1 kcal/mol)
✗ Geometry warnings
✗ Minor protein-contact clashes (4)
✗ Internal clashes (8)
Score
-24.835
kcal/mol
LE
-1.242
kcal/mol/HA
Fit Quality
-10.39
FQ (Leeson)
HAC
20
heavy atoms
MW
266
Da
LogP
3.19
cLogP
Interaction summary
HB 6
HY 9
PI 2
CLASH 1
Interaction summary
HB 6
HY 9
PI 2
CLASH 1
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 | 0.403 | Score | -24.835 |
|---|---|---|---|
| Inter norm | -1.239 | Intra norm | -0.003 |
| Top1000 | no | Excluded | no |
| Contacts | 18 | H-bonds | 6 |
| Artifact reason | geometry warning; 8 clashes; 4 protein contact clashes | ||
| Residues |
ARG137
ARG141
ASN103
HIS102
HIS138
MET98
TYR94
ARG113
ASP10
CYS69
GLY70
GLY72
GLY74
HIS11
ILE73
PRO12
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 | 14 | Native recall | 1.00 |
| Jaccard | 0.78 | RMSD | - |
| HB strict | 5 | Strict recall | 0.42 |
| HB same residue+role | 4 | HB role recall | 0.44 |
| HB same residue | 3 | HB residue recall | 0.38 |
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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 527 | 0.4030490357475004 | -1.23859 | -24.8347 | 6 | 18 | 14 | 1.00 | 0.44 | - | no | Current |
Molecular metrics
RDKit SASA burial, strain energy (MMFF94s), ligand efficiency and fit quality for this docking pose.
Scoring & efficiency
Docking score
-24.835kcal/mol
Ligand efficiency (LE)
-1.2417kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-10.391
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
20HA
Physicochemical properties
Molecular weight
266.3Da
Lipinski: ≤ 500 Da
LogP (cLogP)
3.19
Lipinski: ≤ 5
Rotatable bonds
4
Conformational strain (MMFF94s)
Strain energy (ΔE)
10.07kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
46.82kcal/mol
Minimised FF energy
36.76kcal/mol
SASA & burial
✓ computed
SASA (unbound)
503.9Ų
Total solvent-accessible surface area of free ligand
BSA total
441.6Ų
Buried surface area upon binding
BSA apolar
393.0Ų
Hydrophobic contacts buried
BSA polar
48.6Ų
Polar contacts buried
Fraction buried
87.6%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
89.0%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-2195.0Ų
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
742.3Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)