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
28.6 kcal/mol
Protein clashes
3
Internal clashes
3
Native overlap
contact recall 0.93, Jaccard 0.72, H-bond role recall 0.22
Reason: no major geometry red flags detected
3 protein-contact clashes
3 intramolecular clashes
37% of hydrophobic surface appears solvent-exposed (10/27 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 (-0.749 kcal/mol/HA)
✓ Good fit quality (FQ -7.55)
✓ Strong H-bond network (6 bonds)
✓ Deep burial (76% SASA buried)
✓ Lipophilic contacts well-matched (81%)
✗ High strain energy (28.6 kcal/mol)
✗ Geometry warnings
✗ Many internal clashes (13)
Score
-26.203
kcal/mol
LE
-0.749
kcal/mol/HA
Fit Quality
-7.55
FQ (Leeson)
HAC
35
heavy atoms
MW
472
Da
LogP
4.29
cLogP
Final rank
3.4027
rank score
Inter norm
-0.731
normalised
Contacts
17
H-bonds 9
Interaction summary
HBD 2
HBA 4
HY 3
PI 3
CLASH 3
Interaction summary
HBD 2
HBA 4
HY 3
PI 3
CLASH 3
HBD/HBA · H-bonds (geometric)
HBD = ligand donates H · HBA = ligand accepts H · ~ = weak (≥110°). Mode: strict. Residues: 4.
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 | 13 | Native recall | 0.93 |
| Jaccard | 0.72 | 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
| Pose | Final rank | Inter norm | Score | HB | CT | CT overlap | CT recall | HB role rec. | RMSD | Excluded | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 411 | 1.6227558752177318 | -0.613323 | -21.9414 | 7 | 12 | 0 | 0.00 | 0.00 | - | no | Open |
| 496 | 1.9912733024817217 | -0.773538 | -26.1886 | 7 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 338 | 2.6181443713600236 | -1.04339 | -30.6534 | 8 | 20 | 0 | 0.00 | 0.00 | - | no | Open |
| 401 | 3.402664483712341 | -0.731415 | -26.2033 | 9 | 17 | 13 | 0.93 | 0.22 | - | no | Current |
| 386 | 3.822797838657043 | -0.624919 | -15.0669 | 8 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 365 | 4.081194701767038 | -0.775005 | -28.4625 | 10 | 19 | 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
-26.203kcal/mol
Ligand efficiency (LE)
-0.7487kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-7.551
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
35HA
Physicochemical properties
Molecular weight
471.5Da
Lipinski: ≤ 500 Da
LogP (cLogP)
4.29
Lipinski: ≤ 5
Rotatable bonds
9
Conformational strain (MMFF94s)
Strain energy (ΔE)
28.62kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
72.49kcal/mol
Minimised FF energy
43.87kcal/mol
SASA & burial
✓ computed
SASA (unbound)
684.6Ų
Total solvent-accessible surface area of free ligand
BSA total
522.6Ų
Buried surface area upon binding
BSA apolar
421.8Ų
Hydrophobic contacts buried
BSA polar
100.8Ų
Polar contacts buried
Fraction buried
76.3%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
80.7%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-2271.5Ų
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
759.8Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)