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
Reject
SASA cached
Promising but geometrically suspicious
Binding strong
Geometry low
Native strong
SASA done
Strain ΔE
49.2 kcal/mol
Protein clashes
2
Internal clashes
2
Native overlap
contact recall 0.86, Jaccard 0.71, H-bond role recall 0.44
Reason: strain 49.2 kcal/mol
strain ΔE 49.2 kcal/mol
2 protein-contact clashes
44% of hydrophobic surface appears solvent-exposed (7/16 atoms). Partial exposure is common but may limit selectivity and membrane permeability.
Molecular report
Reject
Multiple quality flags — this pose should be deprioritised or discarded.
✓ Excellent LE (-0.956 kcal/mol/HA)
✓ Good fit quality (FQ -8.80)
✓ Strong H-bond network (11 bonds)
✓ Deep burial (71% SASA buried)
✓ Lipophilic contacts well-matched (69%)
✗ Extreme strain energy (49.2 kcal/mol)
✗ Geometry warnings
✗ Internal clashes (6)
Score
-24.843
kcal/mol
LE
-0.956
kcal/mol/HA
Fit Quality
-8.80
FQ (Leeson)
HAC
26
heavy atoms
MW
378
Da
LogP
0.79
cLogP
Interaction summary
HB 11
HY 1
PI 3
CLASH 2
⚠ Exposure 43%
Interaction summary
HB 11
HY 1
PI 3
CLASH 2
⚠ Exposure 43%
Partial hydrophobic solvent exposure
44% of hydrophobic surface appears solvent-exposed (7/16 atoms). Partial exposure is common but may limit selectivity and membrane permeability.
Non-polar atoms 16
Buried (contacted) 9
Exposed 7
LogP 0.79
H-bonds 11
Exposed fragments:
phenyl (4/6 atoms exposed)aliphatic chain/group (3 atoms exposed)
| Final rank | 2.487 | Score | -24.843 |
|---|---|---|---|
| Inter norm | -1.079 | Intra norm | 0.123 |
| Top1000 | no | Excluded | no |
| Contacts | 15 | H-bonds | 11 |
| Artifact reason | geometry warning; 6 clashes; 1 protein clash; high strain Δ 49.1 | ||
| Residues |
ARG137
ARG140
ARG141
ASN103
HIS102
HIS138
CYS69
GLY70
GLY72
GLY74
HIS11
ILE73
SER43
SER71
TYR46
| ||
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 | ||
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 | 12 | Native recall | 0.86 |
| Jaccard | 0.71 | 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 |
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
All stored poses for this docking hit
| Pose | Final rank | Inter norm | Score | HB | CT | CT overlap | CT recall | HB role rec. | RMSD | Excluded | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 538 | 1.6890420589433734 | -0.876062 | -18.5492 | 5 | 17 | 0 | 0.00 | 0.00 | - | no | Open |
| 578 | 1.7455832875701298 | -1.04513 | -22.1499 | 6 | 14 | 0 | 0.00 | 0.00 | - | no | Open |
| 569 | 1.7724214234298203 | -1.01549 | -23.1894 | 6 | 14 | 0 | 0.00 | 0.00 | - | no | Open |
| 569 | 1.7783840791674765 | -1.0041 | -24.7592 | 6 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 545 | 2.1801023352322155 | -1.14702 | -29.589 | 14 | 14 | 0 | 0.00 | 0.00 | - | no | Open |
| 578 | 2.2950088551183443 | -0.939152 | -19.4559 | 10 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 572 | 2.4866872836960074 | -1.07884 | -24.8429 | 11 | 15 | 12 | 0.86 | 0.44 | - | no | Current |
| 573 | 3.847742802334122 | -0.869936 | -20.868 | 10 | 17 | 0 | 0.00 | 0.00 | - | no | Open |
| 564 | 4.090578712367698 | -0.991863 | -19.9768 | 10 | 13 | 0 | 0.00 | 0.00 | - | no | Open |
| 595 | 4.424815777537417 | -0.904088 | -20.6734 | 8 | 14 | 0 | 0.00 | 0.00 | - | no | Open |
| 550 | 4.437704091940646 | -1.08851 | -28.813 | 14 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 548 | 4.53216170732747 | -1.11454 | -27.9889 | 13 | 18 | 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
-24.843kcal/mol
Ligand efficiency (LE)
-0.9555kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-8.803
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
26HA
Physicochemical properties
Molecular weight
378.4Da
Lipinski: ≤ 500 Da
LogP (cLogP)
0.79
Lipinski: ≤ 5
Rotatable bonds
8
Conformational strain (MMFF94s)
Strain energy (ΔE)
49.19kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
140.56kcal/mol
Minimised FF energy
91.37kcal/mol
SASA & burial
✓ computed
SASA (unbound)
645.3Ų
Total solvent-accessible surface area of free ligand
BSA total
460.2Ų
Buried surface area upon binding
BSA apolar
319.1Ų
Hydrophobic contacts buried
BSA polar
141.1Ų
Polar contacts buried
Fraction buried
71.3%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
69.3%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-2201.7Ų
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
742.4Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)