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
Promising
SASA cached
Promising and worth follow-up
Binding strong
Geometry high
Native strong
SASA done
Strain ΔE
10.2 kcal/mol
Protein clashes
1
Internal clashes
1
Native overlap
contact recall 1.00, Jaccard 0.78, H-bond role recall 0.44
Reason: no major geometry red flags detected
1 protein-contact clashes
Molecular report
Promising
Reasonable quality metrics. Warrants further investigation.
✓ Excellent LE (-1.021 kcal/mol/HA)
✓ Good fit quality (FQ -9.15)
✓ Good H-bonds (5 bonds)
✓ Deep burial (81% SASA buried)
✓ Lipophilic contacts well-matched (80%)
✗ Moderate strain (10.2 kcal/mol)
✗ Geometry warnings
✗ Internal clashes (9)
Score
-24.500
kcal/mol
LE
-1.021
kcal/mol/HA
Fit Quality
-9.15
FQ (Leeson)
HAC
24
heavy atoms
MW
402
Da
LogP
4.42
cLogP
Interaction summary
HB 5
HY 3
PI 4
CLASH 1
Interaction summary
HB 5
HY 3
PI 4
CLASH 1
HB · H-bonds
Mode: strict. Count shows atom-level H-bonds; unique residues in summary: 0.
PI · π–π interactions
Native π–π recall is disabled because no explicit native π–π reference was stored.
HY · Hydrophobic contacts
CLASH · Clashes
| Final rank | 1.778 | Score | -24.500 |
|---|---|---|---|
| Inter norm | -1.071 | Intra norm | 0.050 |
| Top1000 | no | Excluded | no |
| Contacts | 18 | H-bonds | 5 |
| Artifact reason | geometry warning; 9 clashes; 1 protein clash | ||
| Residues |
ARG137
ARG141
ASN103
HIS102
HIS138
MET98
TYR94
ARG113
ASP10
CYS69
GLY70
GLY72
GLY74
HIS11
ILE73
PRO12
SER71
TYR46
| ||
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 | 0.78 | RMSD | - |
| HB strict | 5 | Strict recall | 0.42 |
| HB same residue+role | 4 | HB role recall | 0.44 |
| 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
| Pose | Final rank | Inter norm | Score | HB | CT | CT overlap | CT recall | HB role rec. | RMSD | Excluded | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 29 | 0.13111952234188723 | -1.3806 | -31.136 | 6 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 30 | 0.7591190398503808 | -0.940797 | -16.8599 | 7 | 10 | 0 | 0.00 | 0.00 | - | no | Open |
| 26 | 0.9544002616823256 | -1.29256 | -28.8045 | 8 | 17 | 0 | 0.00 | 0.00 | - | no | Open |
| 19 | 1.1294901416468546 | -1.00522 | -19.339 | 1 | 11 | 0 | 0.00 | 0.00 | - | no | Open |
| 12 | 1.7775808264988386 | -1.07097 | -24.5001 | 5 | 18 | 14 | 1.00 | 0.44 | - | no | Current |
| 23 | 2.9951677238743564 | -1.10745 | -23.6127 | 4 | 10 | 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
-24.500kcal/mol
Ligand efficiency (LE)
-1.0208kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-9.149
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
24HA
Physicochemical properties
Molecular weight
401.6Da
Lipinski: ≤ 500 Da
LogP (cLogP)
4.42
Lipinski: ≤ 5
Rotatable bonds
2
Conformational strain (MMFF94s)
Strain energy (ΔE)
10.22kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
119.69kcal/mol
Minimised FF energy
109.46kcal/mol
SASA & burial
✓ computed
SASA (unbound)
543.7Ų
Total solvent-accessible surface area of free ligand
BSA total
440.1Ų
Buried surface area upon binding
BSA apolar
350.7Ų
Hydrophobic contacts buried
BSA polar
89.4Ų
Polar contacts buried
Fraction buried
80.9%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
79.7%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-2119.6Ų
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
814.6Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)