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 strong
SASA done
Strain ΔE
15.7 kcal/mol
Protein clashes
2
Internal clashes
2
Native overlap
contact recall 1.00, Jaccard 0.78, H-bond role recall 0.44
Reason: no major geometry red flags detected
2 protein-contact clashes
38% of hydrophobic surface appears solvent-exposed (8/21 atoms). Partial exposure is common but may limit selectivity and membrane permeability.
Molecular report
Promising
Reasonable quality metrics. Warrants further investigation.
✓ Excellent LE (-0.572 kcal/mol/HA)
✓ Good fit quality (FQ -5.34)
✓ Strong H-bond network (9 bonds)
✓ Deep burial (72% SASA buried)
✓ Lipophilic contacts well-matched (79%)
✗ Moderate strain (15.7 kcal/mol)
✗ Geometry warnings
✗ Internal clashes (9)
Score
-15.445
kcal/mol
LE
-0.572
kcal/mol/HA
Fit Quality
-5.34
FQ (Leeson)
HAC
27
heavy atoms
MW
368
Da
LogP
3.85
cLogP
Interaction summary
HB 9
HY 9
PI 3
CLASH 2
⚠ Exposure 38%
Interaction summary
HB 9
HY 9
PI 3
CLASH 2
⚠ Exposure 38%
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
38% of hydrophobic surface appears solvent-exposed (8/21 atoms). Partial exposure is common but may limit selectivity and membrane permeability.
Non-polar atoms 21
Buried (contacted) 13
Exposed 8
LogP 3.85
H-bonds 9
Exposed fragments:
aliphatic chain/group (8 atoms exposed)
| Final rank | 4.451 | Score | -15.445 |
|---|---|---|---|
| Inter norm | -0.917 | Intra norm | 0.345 |
| Top1000 | no | Excluded | no |
| Contacts | 18 | H-bonds | 9 |
| Artifact reason | geometry warning; 9 clashes; 3 protein clashes | ||
| Residues |
ARG137
ARG141
ASN103
HIS102
HIS138
MET98
TYR94
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 | 0.78 | RMSD | - |
| HB strict | 6 | Strict recall | 0.50 |
| HB same residue+role | 4 | HB role recall | 0.44 |
| HB same residue | 4 | HB residue recall | 0.50 |
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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 478 | 2.861286354199215 | -0.940821 | -23.6282 | 6 | 17 | 0 | 0.00 | 0.00 | - | no | Open |
| 487 | 3.0517203553181087 | -0.947352 | -24.155 | 6 | 17 | 0 | 0.00 | 0.00 | - | no | Open |
| 83 | 3.6733472529743927 | -0.962715 | -19.9772 | 7 | 19 | 0 | 0.00 | 0.00 | - | no | Open |
| 44 | 4.45065024543268 | -0.91695 | -15.4446 | 9 | 18 | 14 | 1.00 | 0.44 | - | no | Current |
Molecular metrics
RDKit SASA burial, strain energy (MMFF94s), ligand efficiency and fit quality for this docking pose.
Scoring & efficiency
Docking score
-15.445kcal/mol
Ligand efficiency (LE)
-0.5720kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-5.337
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
27HA
Physicochemical properties
Molecular weight
368.4Da
Lipinski: ≤ 500 Da
LogP (cLogP)
3.85
Lipinski: ≤ 5
Rotatable bonds
10
Conformational strain (MMFF94s)
Strain energy (ΔE)
15.71kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
82.67kcal/mol
Minimised FF energy
66.96kcal/mol
SASA & burial
✓ computed
SASA (unbound)
687.3Ų
Total solvent-accessible surface area of free ligand
BSA total
494.4Ų
Buried surface area upon binding
BSA apolar
392.1Ų
Hydrophobic contacts buried
BSA polar
102.3Ų
Polar contacts buried
Fraction buried
71.9%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
79.3%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-2253.2Ų
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
769.2Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)