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
Likely artefact or unreliable pose
Binding weak
Geometry low
Native strong
SASA done
Strain ΔE
57.8 kcal/mol
Protein clashes
3
Internal clashes
3
Native overlap
contact recall 1.00, Jaccard 1.00, H-bond role recall 1.00
Reason: strain 57.8 kcal/mol
strain ΔE 57.8 kcal/mol
3 protein-contact clashes
3 intramolecular clashes
50% of hydrophobic surface appears solvent-exposed (3/6 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.
✓ Strong H-bond network (16 bonds)
✓ Deep burial (87% SASA buried)
✗ Extreme strain energy (57.8 kcal/mol)
HAC
16
heavy atoms
MW
258
Da
LogP
-2.39
cLogP
Interaction summary
HB 16
HY 4
PI 0
CLASH 3
⚠ Exposure 50%
Interaction summary
HB 16
HY 4
PI 0
CLASH 3
⚠ Exposure 50%
HB · H-bonds
Mode: strict. Count shows atom-level H-bonds; unique residues in summary: 0.
PI · π–π interactions
No pi · π–π interactions detected for this pose.
HY · Hydrophobic contacts
CLASH · Clashes
Partial hydrophobic solvent exposure
50% of hydrophobic surface appears solvent-exposed (3/6 atoms). Partial exposure is common but may limit selectivity and membrane permeability.
Non-polar atoms 6
Buried (contacted) 3
Exposed 3
LogP -2.39
H-bonds 16
Exposed fragments:
aliphatic chain/group (3 atoms exposed)
| Final rank | - | Score | - |
|---|---|---|---|
| Inter norm | - | Intra norm | - |
| Top1000 | no | Excluded | no |
| Contacts | 14 | H-bonds | 16 |
| Artifact reason | Native reference ligand | ||
| Residues |
ARG137
ARG141
ASN103
HIS102
HIS138
ASP10
CYS69
GLY70
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 | 1.00 | RMSD | 0.00 Å |
| HB strict | 12 | Strict recall | 1.00 |
| HB same residue+role | 9 | HB role recall | 1.00 |
| HB same residue | 8 | HB residue recall | 1.00 |
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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| - | - | - | - | 16 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| - ★ Native | - | - | - | 16 | 14 | 14 | 1.00 | 1.00 | 0.00 Å | no | Current |
Molecular metrics
RDKit SASA burial, strain energy (MMFF94s), ligand efficiency and fit quality for this docking pose.
Scoring & efficiency
Heavy atom count
16HA
Physicochemical properties
Molecular weight
258.1Da
Lipinski: ≤ 500 Da
LogP (cLogP)
-2.39
Lipinski: ≤ 5
Rotatable bonds
11
Conformational strain (MMFF94s)
Strain energy (ΔE)
57.79kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
48.19kcal/mol
Minimised FF energy
-9.61kcal/mol
SASA & burial
✓ computed
SASA (unbound)
414.2Ų
Total solvent-accessible surface area of free ligand
BSA total
361.8Ų
Buried surface area upon binding
BSA apolar
146.4Ų
Hydrophobic contacts buried
BSA polar
215.4Ų
Polar contacts buried
Fraction buried
87.3%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
40.5%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-1901.8Ų
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
734.8Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)