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 mixed
SASA done
Strain ΔE
16.4 kcal/mol
Protein clashes
2
Internal clashes
2
Native overlap
contact recall 0.50, Jaccard 0.47, H-bond role recall 0.22
Reason: no major geometry red flags detected
2 protein-contact clashes
56% of hydrophobic surface appears solvent-exposed (9/16 atoms). Partial exposure is common but may limit selectivity and membrane permeability.
Molecular report
Promising
Reasonable quality metrics. Warrants further investigation.
✓ Excellent LE (-0.992 kcal/mol/HA)
✓ Good fit quality (FQ -8.46)
✓ Strong H-bond network (10 bonds)
✓ Deep burial (69% SASA buried)
✓ Lipophilic contacts well-matched (77%)
✗ Moderate strain (16.4 kcal/mol)
✗ Geometry warnings
✗ Internal clashes (8)
Score
-20.829
kcal/mol
LE
-0.992
kcal/mol/HA
Fit Quality
-8.46
FQ (Leeson)
HAC
21
heavy atoms
MW
279
Da
LogP
2.88
cLogP
Interaction summary
HB 10
HY 1
PI 3
CLASH 2
⚠ Exposure 56%
Interaction summary
HB 10
HY 1
PI 3
CLASH 2
⚠ Exposure 56%
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
56% of hydrophobic surface appears solvent-exposed (9/16 atoms). Partial exposure is common but may limit selectivity and membrane permeability.
Non-polar atoms 16
Buried (contacted) 7
Exposed 9
LogP 2.88
H-bonds 10
Exposed fragments:
phenyl (6/6 atoms exposed)aliphatic chain/group (3 atoms exposed)
| Final rank | 4.217 | Score | -20.829 |
|---|---|---|---|
| Inter norm | -1.176 | Intra norm | 0.184 |
| Top1000 | no | Excluded | no |
| Contacts | 8 | H-bonds | 10 |
| Artifact reason | geometry warning; 8 clashes; 3 protein clashes | ||
| Residues |
ARG137
ARG141
ASN103
HIS102
HIS138
HIS11
SER43
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 | 7 | Native recall | 0.50 |
| Jaccard | 0.47 | 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 36 | 3.0144044091666906 | -1.30376 | -21.2924 | 9 | 14 | 0 | 0.00 | 0.00 | - | no | Open |
| 64 | 4.216724923599552 | -1.17602 | -20.829 | 10 | 8 | 7 | 0.50 | 0.22 | - | no | Current |
Molecular metrics
RDKit SASA burial, strain energy (MMFF94s), ligand efficiency and fit quality for this docking pose.
Scoring & efficiency
Docking score
-20.829kcal/mol
Ligand efficiency (LE)
-0.9919kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-8.460
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
21HA
Physicochemical properties
Molecular weight
279.3Da
Lipinski: ≤ 500 Da
LogP (cLogP)
2.88
Lipinski: ≤ 5
Rotatable bonds
5
Conformational strain (MMFF94s)
Strain energy (ΔE)
16.43kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
25.21kcal/mol
Minimised FF energy
8.78kcal/mol
SASA & burial
✓ computed
SASA (unbound)
517.6Ų
Total solvent-accessible surface area of free ligand
BSA total
356.1Ų
Buried surface area upon binding
BSA apolar
273.2Ų
Hydrophobic contacts buried
BSA polar
82.9Ų
Polar contacts buried
Fraction buried
68.8%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
76.7%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-2142.0Ų
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
768.8Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)