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
38.2 kcal/mol
Protein clashes
5
Internal clashes
5
Native overlap
contact recall 0.93, Jaccard 0.81, H-bond role recall 0.33
Reason: no major geometry red flags detected
5 protein-contact clashes
5 intramolecular clashes
Molecular report
Weak
Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-0.727 kcal/mol/HA)
✓ Good fit quality (FQ -6.79)
✓ Good H-bonds (5 bonds)
✓ Deep burial (73% SASA buried)
✓ Lipophilic contacts well-matched (77%)
✗ Very high strain energy (38.2 kcal/mol)
✗ Geometry warnings
✗ Many internal clashes (10)
Score
-19.637
kcal/mol
LE
-0.727
kcal/mol/HA
Fit Quality
-6.79
FQ (Leeson)
HAC
27
heavy atoms
MW
359
Da
LogP
3.72
cLogP
Final rank
3.6761
rank score
Inter norm
-0.891
normalised
Contacts
15
H-bonds 8
Interaction summary
HBA 5
HY 2
PI 3
CLASH 5
Interaction summary
HBA 5
HY 2
PI 3
CLASH 5
HBD/HBA · H-bonds (geometric)
HBD = ligand donates H · HBA = ligand accepts H · ~ = weak (≥110°). Mode: permissive. Residues: 3.
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: permissive.
| 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 | 0.81 | RMSD | - |
| HB strict | 4 | Strict recall | 0.33 |
| HB same residue+role | 3 | HB role recall | 0.33 |
| 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
Molecular metrics
RDKit SASA burial, strain energy (MMFF94s), ligand efficiency and fit quality for this docking pose.
Scoring & efficiency
Docking score
-19.637kcal/mol
Ligand efficiency (LE)
-0.7273kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-6.785
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
27HA
Physicochemical properties
Molecular weight
359.4Da
Lipinski: ≤ 500 Da
LogP (cLogP)
3.72
Lipinski: ≤ 5
Rotatable bonds
4
Conformational strain (MMFF94s)
Strain energy (ΔE)
38.16kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
67.30kcal/mol
Minimised FF energy
29.14kcal/mol
SASA & burial
✓ computed
SASA (unbound)
614.2Ų
Total solvent-accessible surface area of free ligand
BSA total
449.5Ų
Buried surface area upon binding
BSA apolar
347.6Ų
Hydrophobic contacts buried
BSA polar
101.9Ų
Polar contacts buried
Fraction buried
73.2%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
77.3%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-2239.5Ų
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
741.6Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)