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
Weak
SASA cached
Promising but geometrically suspicious
Binding strong
Geometry low
Native strong
SASA done
Strain ΔE
25.7 kcal/mol
Protein clashes
4
Internal clashes
7
Native overlap
contact recall 0.93, Jaccard 0.87, H-bond role recall 0.44
Reason: 7 internal clashes
4 protein-contact clashes
7 intramolecular clashes
38% of hydrophobic surface appears solvent-exposed (6/16 atoms). Partial exposure is common but may limit selectivity and membrane permeability.
Molecular report
Weak
Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-1.102 kcal/mol/HA)
✓ Good fit quality (FQ -9.72)
✓ Good H-bonds (5 bonds)
✓ Deep burial (67% SASA buried)
✓ Lipophilic contacts well-matched (72%)
✗ High strain energy (25.7 kcal/mol)
✗ Geometry warnings
✗ Minor protein-contact clashes (4)
✗ Internal clashes (7)
Score
-25.339
kcal/mol
LE
-1.102
kcal/mol/HA
Fit Quality
-9.72
FQ (Leeson)
HAC
23
heavy atoms
MW
347
Da
LogP
2.29
cLogP
Final rank
0.3607
rank score
Inter norm
-1.123
normalised
Contacts
14
H-bonds 10
Interaction summary
HBD 1
HBA 4
HY 3
PI 2
CLASH 0
Interaction summary
HBD 1
HBA 4
HY 3
PI 2
CLASH 0
HBD/HBA · H-bonds (geometric)
HBD = ligand donates H · HBA = ligand accepts H · ~ = weak (≥110°). Mode: strict. Residues: 5.
PI · π–π interactions
Native π–π recall is disabled because no explicit native π–π reference was stored.
HY · Hydrophobic contacts
CLASH · Clashes
No clash · clashes detected for this pose.
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 | 0.87 | RMSD | - |
| HB strict | 5 | Strict recall | 0.42 |
| HB same residue+role | 4 | HB role recall | 0.44 |
| 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
| Pose | Final rank | Inter norm | Score | HB | CT | CT overlap | CT recall | HB role rec. | RMSD | Excluded | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 545 | 0.36070520263121236 | -1.12281 | -25.3388 | 10 | 14 | 13 | 0.93 | 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
-25.339kcal/mol
Ligand efficiency (LE)
-1.1017kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-9.723
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
23HA
Physicochemical properties
Molecular weight
347.5Da
Lipinski: ≤ 500 Da
LogP (cLogP)
2.29
Lipinski: ≤ 5
Rotatable bonds
3
Conformational strain (MMFF94s)
Strain energy (ΔE)
25.66kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
65.32kcal/mol
Minimised FF energy
39.66kcal/mol
SASA & burial
✓ computed
SASA (unbound)
584.1Ų
Total solvent-accessible surface area of free ligand
BSA total
391.5Ų
Buried surface area upon binding
BSA apolar
281.6Ų
Hydrophobic contacts buried
BSA polar
109.9Ų
Polar contacts buried
Fraction buried
67.0%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
71.9%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-2143.9Ų
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
763.8Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)