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
20.4 kcal/mol
Protein clashes
3
Internal clashes
3
Native overlap
contact recall 1.00, Jaccard 0.82, H-bond role recall 0.67
Reason: no major geometry red flags detected
3 protein-contact clashes
3 intramolecular clashes
Molecular report
Weak
Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-1.245 kcal/mol/HA)
✓ Good fit quality (FQ -10.21)
✓ Strong H-bond network (7 bonds)
✓ Deep burial (89% SASA buried)
✓ Lipophilic contacts well-matched (70%)
✗ High strain energy (20.4 kcal/mol)
✗ Geometry warnings
Score
-23.655
kcal/mol
LE
-1.245
kcal/mol/HA
Fit Quality
-10.21
FQ (Leeson)
HAC
19
heavy atoms
MW
279
Da
LogP
1.39
cLogP
Final rank
3.1648
rank score
Inter norm
-1.341
normalised
Contacts
17
H-bonds 9
Interaction summary
HBD 2
HBA 5
HY 3
PI 3
CLASH 3
Interaction summary
HBD 2
HBA 5
HY 3
PI 3
CLASH 3
HBD/HBA · H-bonds (geometric)
HBD = ligand donates H · HBA = ligand accepts H · ~ = weak (≥110°). Mode: strict. Residues: 7.
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 | 14 | Native recall | 1.00 |
| Jaccard | 0.82 | RMSD | - |
| HB strict | 6 | Strict recall | 0.50 |
| HB same residue+role | 6 | HB role recall | 0.67 |
| HB same residue | 7 | HB residue recall | 0.88 |
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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 551 | 3.1648334261698836 | -1.34099 | -23.6548 | 9 | 17 | 14 | 1.00 | 0.67 | - | no | Current |
| 559 | 3.8013867832757016 | -1.17795 | -19.1385 | 9 | 13 | 0 | 0.00 | 0.00 | - | no | Open |
Molecular metrics
RDKit SASA burial, strain energy (MMFF94s), ligand efficiency and fit quality for this docking pose.
Scoring & efficiency
Docking score
-23.655kcal/mol
Ligand efficiency (LE)
-1.2450kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-10.205
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
19HA
Physicochemical properties
Molecular weight
279.3Da
Lipinski: ≤ 500 Da
LogP (cLogP)
1.39
Lipinski: ≤ 5
Rotatable bonds
4
Conformational strain (MMFF94s)
Strain energy (ΔE)
20.40kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
90.35kcal/mol
Minimised FF energy
69.95kcal/mol
SASA & burial
✓ computed
SASA (unbound)
495.9Ų
Total solvent-accessible surface area of free ligand
BSA total
442.4Ų
Buried surface area upon binding
BSA apolar
310.4Ų
Hydrophobic contacts buried
BSA polar
131.9Ų
Polar contacts buried
Fraction buried
89.2%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
70.2%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-2083.0Ų
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
742.7Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)