Molecular metrics status: done
RDKit SASA-based burial metrics are cached.
SASA cached
3D complex viewer
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Protein receptor
Pocket residues
Cofactor context
Docked ligand
Overall assessment
Weak
SASA cached
Weak or marginal quality
Binding strong
Geometry high
Native strong
SASA done
Strain ΔE
26.2 kcal/mol
Protein clashes
1
Internal clashes
1
Native overlap
contact recall 0.93, Jaccard 0.72, H-bond role recall 0.44
Reason: no major geometry red flags detected
1 protein-contact clashes
62% of hydrophobic surface is solvent-exposed (15/24 atoms). Large non-polar area without protein contacts incurs a desolvation penalty and will reduce binding affinity. Consider truncating or replacing the exposed fragment.
Molecular report
Weak
Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-0.681 kcal/mol/HA)
✓ Good fit quality (FQ -6.63)
✓ Good H-bonds (5 bonds)
✓ Deep burial (69% SASA buried)
✓ Lipophilic contacts well-matched (78%)
✗ High strain energy (26.2 kcal/mol)
✗ Geometry warnings
✗ Many internal clashes (13)
Score
-21.098
kcal/mol
LE
-0.681
kcal/mol/HA
Fit Quality
-6.63
FQ (Leeson)
HAC
31
heavy atoms
MW
445
Da
LogP
4.09
cLogP
Interaction summary
HB 5
HY 5
PI 1
CLASH 1
⚠ Exposure 62%
Interaction summary
HB 5
HY 5
PI 1
CLASH 1
⚠ Exposure 62%
Solvent-exposed hydrophobic surface — desolvation penalty likely
62% of hydrophobic surface is solvent-exposed (15/24 atoms). Large non-polar area without protein contacts incurs a desolvation penalty and will reduce binding affinity. Consider truncating or replacing the exposed fragment.
Non-polar atoms 24
Buried (contacted) 9
Exposed 15
LogP 4.09
H-bonds 5
Exposed fragments:
phenyl (6/6 atoms exposed)phenyl (5/6 atoms exposed)aliphatic chain/group (6 atoms exposed)
| Final rank | 2.619 | Score | -21.098 |
|---|---|---|---|
| Inter norm | -0.773 | Intra norm | 0.093 |
| Top1000 | no | Excluded | no |
| Contacts | 17 | H-bonds | 5 |
| Artifact reason | geometry warning; 13 clashes; 1 protein clash; moderate strain Δ 26.2 | ||
| Residues |
ARG137
ARG141
ASN103
HIS102
MET98
TYR94
ARG113
ASP10
CYS69
GLY70
GLY72
GLY74
HIS11
ILE73
PRO12
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 | 13 | Native recall | 0.93 |
| Jaccard | 0.72 | RMSD | - |
| HB strict | 4 | Strict recall | 0.33 |
| 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 323 | 1.8374890049150154 | -0.969584 | -28.9042 | 2 | 19 | 0 | 0.00 | 0.00 | - | no | Open |
| 248 | 1.9941384867362866 | -1.08957 | -30.0306 | 5 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 304 | 2.211946684661809 | -0.948063 | -27.7339 | 2 | 19 | 0 | 0.00 | 0.00 | - | no | Open |
| 263 | 2.61929779556313 | -0.773136 | -21.098 | 5 | 17 | 13 | 0.93 | 0.44 | - | no | Current |
| 303 | 2.98134114670498 | -0.604344 | -17.8172 | 4 | 11 | 0 | 0.00 | 0.00 | - | no | Open |
| 222 | 4.423284701511489 | -1.07428 | -28.5081 | 6 | 21 | 0 | 0.00 | 0.00 | - | no | Open |
| 182 | 4.436297934854 | -1.04887 | -26.4713 | 6 | 21 | 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
-21.098kcal/mol
Ligand efficiency (LE)
-0.6806kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-6.630
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
31HA
Physicochemical properties
Molecular weight
444.6Da
Lipinski: ≤ 500 Da
LogP (cLogP)
4.09
Lipinski: ≤ 5
Rotatable bonds
6
Conformational strain (MMFF94s)
Strain energy (ΔE)
26.15kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
31.06kcal/mol
Minimised FF energy
4.91kcal/mol
SASA & burial
✓ computed
SASA (unbound)
702.0Ų
Total solvent-accessible surface area of free ligand
BSA total
484.6Ų
Buried surface area upon binding
BSA apolar
378.7Ų
Hydrophobic contacts buried
BSA polar
105.9Ų
Polar contacts buried
Fraction buried
69.0%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
78.2%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-2328.3Ų
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
749.8Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)