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
Weak or marginal quality
Binding strong
Geometry medium
Native strong
SASA done
Strain ΔE
36.0 kcal/mol
Protein clashes
1
Internal clashes
1
Native overlap
contact recall 0.64, Jaccard 0.56, H-bond role recall 0.22
Reason: no major geometry red flags detected
1 protein-contact clashes
38% of hydrophobic surface appears solvent-exposed (10/26 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 (-0.681 kcal/mol/HA)
✓ Good fit quality (FQ -6.81)
✓ Strong H-bond network (8 bonds)
✓ Deep burial (67% SASA buried)
✓ Lipophilic contacts well-matched (91%)
✗ Very high strain energy (36.0 kcal/mol)
✗ Geometry warnings
✗ Many internal clashes (15)
Score
-23.149
kcal/mol
LE
-0.681
kcal/mol/HA
Fit Quality
-6.81
FQ (Leeson)
HAC
34
heavy atoms
MW
460
Da
LogP
3.19
cLogP
Final rank
3.9716
rank score
Inter norm
-0.773
normalised
Contacts
11
H-bonds 8
Interaction summary
HBD 3
HBA 5
HY 3
PI 4
CLASH 1
Interaction summary
HBD 3
HBA 5
HY 3
PI 4
CLASH 1
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
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 | 9 | Native recall | 0.64 |
| Jaccard | 0.56 | RMSD | - |
| HB strict | 3 | Strict recall | 0.25 |
| HB same residue+role | 2 | HB role recall | 0.22 |
| HB same residue | 2 | HB residue recall | 0.25 |
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
-23.149kcal/mol
Ligand efficiency (LE)
-0.6809kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-6.813
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
34HA
Physicochemical properties
Molecular weight
459.6Da
Lipinski: ≤ 500 Da
LogP (cLogP)
3.19
Lipinski: ≤ 5
Rotatable bonds
8
Conformational strain (MMFF94s)
Strain energy (ΔE)
36.02kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
-33.88kcal/mol
Minimised FF energy
-69.90kcal/mol
SASA & burial
✓ computed
SASA (unbound)
718.4Ų
Total solvent-accessible surface area of free ligand
BSA total
482.7Ų
Buried surface area upon binding
BSA apolar
437.9Ų
Hydrophobic contacts buried
BSA polar
44.8Ų
Polar contacts buried
Fraction buried
67.2%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
90.7%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-2325.5Ų
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
814.7Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)