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
62.3 kcal/mol
Protein clashes
2
Internal clashes
2
Native overlap
contact recall 0.86, Jaccard 0.75, H-bond role recall 0.22
Reason: strain 62.3 kcal/mol
strain ΔE 62.3 kcal/mol
2 protein-contact clashes
35% of hydrophobic surface appears solvent-exposed (6/17 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 (-0.878 kcal/mol/HA)
✓ Good fit quality (FQ -8.38)
✓ Strong H-bond network (13 bonds)
✓ Deep burial (68% SASA buried)
✓ Lipophilic contacts well-matched (62%)
✗ Extreme strain energy (62.3 kcal/mol)
✗ Geometry warnings
✗ Many internal clashes (12)
Score
-25.451
kcal/mol
LE
-0.878
kcal/mol/HA
Fit Quality
-8.38
FQ (Leeson)
HAC
29
heavy atoms
MW
434
Da
LogP
2.24
cLogP
Interaction summary
HB 13
HY 3
PI 2
CLASH 2
⚠ Exposure 35%
Interaction summary
HB 13
HY 3
PI 2
CLASH 2
⚠ Exposure 35%
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
Partial hydrophobic solvent exposure
35% of hydrophobic surface appears solvent-exposed (6/17 atoms). Partial exposure is common but may limit selectivity and membrane permeability.
Non-polar atoms 17
Buried (contacted) 11
Exposed 6
LogP 2.24
H-bonds 13
Exposed fragments:
phenyl (6/6 atoms exposed)
| Final rank | 3.035 | Score | -25.451 |
|---|---|---|---|
| Inter norm | -0.845 | Intra norm | -0.032 |
| Top1000 | no | Excluded | no |
| Contacts | 14 | H-bonds | 13 |
| Artifact reason | geometry warning; 12 clashes; 1 protein clash; high strain Δ 61.9 | ||
| Residues |
ARG137
ARG141
ASN103
HIS102
HIS138
MET98
TYR94
ASP10
CYS69
GLY70
HIS11
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 | 12 | Native recall | 0.86 |
| Jaccard | 0.75 | RMSD | - |
| HB strict | 4 | Strict recall | 0.33 |
| 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 348 | 0.8052625623810137 | -0.956826 | -26.5786 | 1 | 13 | 0 | 0.00 | 0.00 | - | no | Open |
| 330 | 1.329263884816044 | -0.859526 | -24.8294 | 4 | 17 | 0 | 0.00 | 0.00 | - | no | Open |
| 326 | 2.453092962966273 | -0.93103 | -26.9955 | 10 | 12 | 0 | 0.00 | 0.00 | - | no | Open |
| 376 | 2.4975808499608676 | -0.967058 | -25.9968 | 4 | 17 | 0 | 0.00 | 0.00 | - | no | Open |
| 397 | 2.750322901945091 | -1.0068 | -27.2349 | 6 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 286 | 2.8402209002504564 | -1.18094 | -33.1271 | 8 | 21 | 0 | 0.00 | 0.00 | - | no | Open |
| 340 | 3.0348573502876355 | -0.845126 | -25.451 | 13 | 14 | 12 | 0.86 | 0.22 | - | no | Current |
| 307 | 3.364737405609164 | -1.16289 | -34.6979 | 10 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 383 | 3.6446324022786087 | -0.978854 | -27.1972 | 6 | 14 | 0 | 0.00 | 0.00 | - | no | Open |
| 372 | 4.744139486087101 | -0.827695 | -24.2166 | 8 | 20 | 0 | 0.00 | 0.00 | - | no | Open |
| 292 | 5.145683840208263 | -1.07823 | -23.7962 | 10 | 13 | 0 | 0.00 | 0.00 | - | no | Open |
| 299 | 6.264571217814828 | -0.9861 | -22.256 | 10 | 23 | 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
-25.451kcal/mol
Ligand efficiency (LE)
-0.8776kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-8.378
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
29HA
Physicochemical properties
Molecular weight
434.5Da
Lipinski: ≤ 500 Da
LogP (cLogP)
2.24
Lipinski: ≤ 5
Rotatable bonds
8
Conformational strain (MMFF94s)
Strain energy (ΔE)
62.28kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
-26.66kcal/mol
Minimised FF energy
-88.94kcal/mol
SASA & burial
✓ computed
SASA (unbound)
649.5Ų
Total solvent-accessible surface area of free ligand
BSA total
443.3Ų
Buried surface area upon binding
BSA apolar
274.5Ų
Hydrophobic contacts buried
BSA polar
168.8Ų
Polar contacts buried
Fraction buried
68.3%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
61.9%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-2134.0Ų
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
752.4Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)