Molecular metrics status: done
RDKit SASA-based burial metrics are cached.
SASA cached
3D complex viewer
Viewer legend
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
22.4 kcal/mol
Protein clashes
0
Internal clashes
11
Native overlap
contact recall 0.93, Jaccard 0.76, H-bond role recall 0.44
Reason: 11 internal clashes
11 intramolecular clashes
Molecular report
Weak
Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-0.770 kcal/mol/HA)
✓ Good fit quality (FQ -7.43)
✓ Good H-bonds (3 bonds)
✓ Deep burial (70% SASA buried)
✗ High strain energy (22.4 kcal/mol)
✗ Geometry warnings
✗ Many internal clashes (11)
Score
-23.096
kcal/mol
LE
-0.770
kcal/mol/HA
Fit Quality
-7.43
FQ (Leeson)
HAC
30
heavy atoms
MW
457
Da
LogP
4.07
cLogP
Final rank
2.1394
rank score
Inter norm
-0.812
normalised
Contacts
16
H-bonds 10
Interaction summary
HBA 3
HY 3
PI 3
CLASH 0
Interaction summary
HBA 3
HY 3
PI 3
CLASH 0
HBD/HBA · H-bonds (geometric)
HBD = ligand donates H · HBA = ligand accepts H · ~ = weak (≥110°). Mode: strict. 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
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 | 0.76 | RMSD | - |
| HB strict | 5 | Strict recall | 0.42 |
| HB same residue+role | 4 | HB role recall | 0.44 |
| HB same residue | 4 | HB residue recall | 0.50 |
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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 317 | 1.2591950220038957 | -0.929606 | -25.0038 | 5 | 18 | 0 | 0.00 | 0.00 | - | no | Open |
| 303 | 1.4349598201931029 | -0.831348 | -17.8132 | 3 | 12 | 0 | 0.00 | 0.00 | - | no | Open |
| 318 | 1.4799198755601055 | -0.914004 | -26.8537 | 3 | 19 | 0 | 0.00 | 0.00 | - | no | Open |
| 279 | 2.1393849350164285 | -0.81219 | -23.0963 | 10 | 16 | 13 | 0.93 | 0.44 | - | no | Current |
| 386 | 2.9618795076248428 | -0.838018 | -21.3376 | 5 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 199 | 4.964385884425539 | -0.94066 | -29.9543 | 8 | 17 | 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
-23.096kcal/mol
Ligand efficiency (LE)
-0.7699kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-7.426
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
30HA
Physicochemical properties
Molecular weight
456.6Da
Lipinski: ≤ 500 Da
LogP (cLogP)
4.07
Lipinski: ≤ 5
Rotatable bonds
6
Conformational strain (MMFF94s)
Strain energy (ΔE)
22.36kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
52.98kcal/mol
Minimised FF energy
30.62kcal/mol
SASA & burial
✓ computed
SASA (unbound)
684.5Ų
Total solvent-accessible surface area of free ligand
BSA total
481.5Ų
Buried surface area upon binding
BSA apolar
279.5Ų
Hydrophobic contacts buried
BSA polar
202.0Ų
Polar contacts buried
Fraction buried
70.3%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
58.1%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-2163.6Ų
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
758.8Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)