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 medium
Native strong
SASA done
Strain ΔE
17.9 kcal/mol
Protein clashes
3
Internal clashes
3
Native overlap
contact recall 1.00, Jaccard 0.82, H-bond role recall 0.56
Reason: no major geometry red flags detected
3 protein-contact clashes
3 intramolecular clashes
Molecular report
Promising
Reasonable quality metrics. Warrants further investigation.
✓ Excellent LE (-0.862 kcal/mol/HA)
✓ Good fit quality (FQ -8.05)
✓ Strong H-bond network (10 bonds)
✓ Deep burial (75% SASA buried)
✓ Lipophilic contacts well-matched (78%)
✗ Moderate strain (17.9 kcal/mol)
✗ Geometry warnings
✗ Internal clashes (7)
Score
-23.285
kcal/mol
LE
-0.862
kcal/mol/HA
Fit Quality
-8.05
FQ (Leeson)
HAC
27
heavy atoms
MW
394
Da
LogP
1.81
cLogP
Interaction summary
HB 10
HY 9
PI 3
CLASH 3
Interaction summary
HB 10
HY 9
PI 3
CLASH 3
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 | 2.585 | Score | -23.285 |
|---|---|---|---|
| Inter norm | -0.907 | Intra norm | 0.045 |
| Top1000 | no | Excluded | no |
| Contacts | 17 | H-bonds | 10 |
| Artifact reason | geometry warning; 7 clashes; 1 protein clash | ||
| Residues |
ARG137
ARG141
ASN103
HIS102
HIS138
MET98
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 | 0.82 | RMSD | - |
| HB strict | 6 | Strict recall | 0.50 |
| HB same residue+role | 5 | HB role recall | 0.56 |
| HB same residue | 5 | HB residue recall | 0.62 |
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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 71 | 0.3760571057301034 | -1.0325 | -30.4005 | 11 | 12 | 0 | 0.00 | 0.00 | - | no | Open |
| 58 | 1.0304108529340756 | -1.16052 | -31.0795 | 6 | 18 | 0 | 0.00 | 0.00 | - | no | Open |
| 99 | 1.816352109006644 | -1.19614 | -32.6755 | 5 | 18 | 0 | 0.00 | 0.00 | - | no | Open |
| 97 | 2.1905649553176523 | -0.774236 | -19.1478 | 9 | 13 | 0 | 0.00 | 0.00 | - | no | Open |
| 65 | 2.5848210356258168 | -0.907266 | -23.2853 | 10 | 17 | 14 | 1.00 | 0.56 | - | no | Current |
| 105 | 2.8188096670692153 | -0.81193 | -22.222 | 6 | 11 | 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
-23.285kcal/mol
Ligand efficiency (LE)
-0.8624kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-8.046
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
27HA
Physicochemical properties
Molecular weight
393.8Da
Lipinski: ≤ 500 Da
LogP (cLogP)
1.81
Lipinski: ≤ 5
Rotatable bonds
6
Conformational strain (MMFF94s)
Strain energy (ΔE)
17.87kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
114.96kcal/mol
Minimised FF energy
97.09kcal/mol
SASA & burial
✓ computed
SASA (unbound)
602.6Ų
Total solvent-accessible surface area of free ligand
BSA total
451.6Ų
Buried surface area upon binding
BSA apolar
350.4Ų
Hydrophobic contacts buried
BSA polar
101.2Ų
Polar contacts buried
Fraction buried
74.9%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
77.6%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-2157.7Ų
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
823.0Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)