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 medium
Native strong
SASA done
Strain ΔE
31.3 kcal/mol
Protein clashes
2
Internal clashes
2
Native overlap
contact recall 0.93, Jaccard 0.68, H-bond role recall 0.56
Reason: no major geometry red flags detected
2 protein-contact clashes
40% of hydrophobic surface appears solvent-exposed (10/25 atoms). Partial exposure is common but may limit selectivity and membrane permeability.
Molecular report
Weak
Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-0.800 kcal/mol/HA)
✓ Good fit quality (FQ -7.94)
✓ Strong H-bond network (12 bonds)
✓ Deep burial (73% SASA buried)
✓ Lipophilic contacts well-matched (86%)
✗ Very high strain energy (31.3 kcal/mol)
✗ Geometry warnings
✗ Many internal clashes (10)
Score
-26.395
kcal/mol
LE
-0.800
kcal/mol/HA
Fit Quality
-7.94
FQ (Leeson)
HAC
33
heavy atoms
MW
444
Da
LogP
1.91
cLogP
Interaction summary
HB 12
HY 7
PI 3
CLASH 2
⚠ Exposure 40%
Interaction summary
HB 12
HY 7
PI 3
CLASH 2
⚠ Exposure 40%
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
40% of hydrophobic surface appears solvent-exposed (10/25 atoms). Partial exposure is common but may limit selectivity and membrane permeability.
Non-polar atoms 25
Buried (contacted) 15
Exposed 10
LogP 1.91
H-bonds 12
Exposed fragments:
phenyl (6/6 atoms exposed)aliphatic chain/group (4 atoms exposed)
| Final rank | 3.522 | Score | -26.395 |
|---|---|---|---|
| Inter norm | -0.810 | Intra norm | 0.010 |
| Top1000 | no | Excluded | no |
| Contacts | 18 | H-bonds | 12 |
| Artifact reason | geometry warning; 10 clashes; 2 protein clashes; high strain Δ 31.3 | ||
| Residues |
ARG137
ARG140
ARG141
ASN103
HIS102
ARG113
ASP10
ASP45
CYS69
GLY70
GLY74
HIS11
ILE73
MET75
PRO12
SER43
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 | 13 | Native recall | 0.93 |
| Jaccard | 0.68 | RMSD | - |
| HB strict | 6 | Strict recall | 0.50 |
| HB same residue+role | 5 | HB role recall | 0.56 |
| HB same residue | 5 | HB residue recall | 0.62 |
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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 124 | 2.0144108354324066 | -0.687857 | -22.4649 | 2 | 14 | 0 | 0.00 | 0.00 | - | no | Open |
| 159 | 2.9075038331576377 | -0.919278 | -28.6542 | 4 | 17 | 0 | 0.00 | 0.00 | - | no | Open |
| 112 | 3.521664373030953 | -0.809606 | -26.3949 | 12 | 18 | 13 | 0.93 | 0.56 | - | no | Current |
| 106 | 5.9470200544350105 | -0.860551 | -23.0065 | 12 | 20 | 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
-26.395kcal/mol
Ligand efficiency (LE)
-0.7998kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-7.936
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
33HA
Physicochemical properties
Molecular weight
443.6Da
Lipinski: ≤ 500 Da
LogP (cLogP)
1.91
Lipinski: ≤ 5
Rotatable bonds
8
Conformational strain (MMFF94s)
Strain energy (ΔE)
31.28kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
15.55kcal/mol
Minimised FF energy
-15.73kcal/mol
SASA & burial
✓ computed
SASA (unbound)
747.7Ų
Total solvent-accessible surface area of free ligand
BSA total
544.4Ų
Buried surface area upon binding
BSA apolar
469.5Ų
Hydrophobic contacts buried
BSA polar
74.9Ų
Polar contacts buried
Fraction buried
72.8%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
86.2%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-2418.4Ų
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
736.4Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)