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
14.6 kcal/mol
Protein clashes
1
Internal clashes
1
Native overlap
contact recall 1.00, Jaccard 0.93, H-bond role recall 0.56
Reason: no major geometry red flags detected
1 protein-contact clashes
Molecular report
Promising
Reasonable quality metrics. Warrants further investigation.
✓ Excellent LE (-1.313 kcal/mol/HA)
✓ Good fit quality (FQ -10.76)
✓ Strong H-bond network (11 bonds)
✓ Deep burial (84% SASA buried)
✓ Lipophilic contacts well-matched (75%)
✗ Moderate strain (14.6 kcal/mol)
✗ Geometry warnings
✗ Internal clashes (5)
Score
-24.945
kcal/mol
LE
-1.313
kcal/mol/HA
Fit Quality
-10.76
FQ (Leeson)
HAC
19
heavy atoms
MW
269
Da
LogP
-1.00
cLogP
Interaction summary
HB 11
HY 7
PI 3
CLASH 1
Interaction summary
HB 11
HY 7
PI 3
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 | 3.579 | Score | -24.945 |
|---|---|---|---|
| Inter norm | -1.291 | Intra norm | -0.021 |
| Top1000 | no | Excluded | no |
| Contacts | 15 | H-bonds | 11 |
| Artifact reason | geometry warning; 5 clashes; 3 protein clashes | ||
| Residues |
ARG137
ARG141
ASN103
HIS102
HIS138
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 | 0.93 | RMSD | - |
| HB strict | 6 | Strict recall | 0.50 |
| HB same residue+role | 5 | HB role recall | 0.56 |
| HB same residue | 5 | HB residue recall | 0.62 |
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
Molecular metrics
RDKit SASA burial, strain energy (MMFF94s), ligand efficiency and fit quality for this docking pose.
Scoring & efficiency
Docking score
-24.945kcal/mol
Ligand efficiency (LE)
-1.3129kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-10.761
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
19HA
Physicochemical properties
Molecular weight
269.2Da
Lipinski: ≤ 500 Da
LogP (cLogP)
-1.00
Lipinski: ≤ 5
Rotatable bonds
5
Conformational strain (MMFF94s)
Strain energy (ΔE)
14.56kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
55.34kcal/mol
Minimised FF energy
40.79kcal/mol
SASA & burial
✓ computed
SASA (unbound)
456.6Ų
Total solvent-accessible surface area of free ligand
BSA total
384.8Ų
Buried surface area upon binding
BSA apolar
289.5Ų
Hydrophobic contacts buried
BSA polar
95.3Ų
Polar contacts buried
Fraction buried
84.3%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
75.2%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-2077.2Ų
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
743.4Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)