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
Promising but geometrically suspicious
Binding strong
Geometry low
Native strong
SASA done
Strain ΔE
23.8 kcal/mol
Protein clashes
12
Internal clashes
12
Native overlap
contact recall 0.79, Jaccard 0.55, H-bond role recall 0.33
Reason: 12 protein-contact clashes, 12 internal clashes
12 protein-contact clashes
12 intramolecular clashes
47% of hydrophobic surface appears solvent-exposed (9/19 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 (-0.921 kcal/mol/HA)
✓ Good fit quality (FQ -8.59)
✓ Strong H-bond network (12 bonds)
✓ Deep burial (80% SASA buried)
✓ Lipophilic contacts well-matched (74%)
✗ High strain energy (23.8 kcal/mol)
✗ Geometry warnings
✗ Internal clashes (7)
Score
-24.871
kcal/mol
LE
-0.921
kcal/mol/HA
Fit Quality
-8.59
FQ (Leeson)
HAC
27
heavy atoms
MW
430
Da
LogP
2.31
cLogP
Interaction summary
HB 12
HY 10
PI 2
CLASH 12
⚠ Exposure 47%
Interaction summary
HB 12
HY 10
PI 2
CLASH 12
⚠ Exposure 47%
Partial hydrophobic solvent exposure
47% of hydrophobic surface appears solvent-exposed (9/19 atoms). Partial exposure is common but may limit selectivity and membrane permeability.
Non-polar atoms 19
Buried (contacted) 10
Exposed 9
LogP 2.31
H-bonds 12
Exposed fragments:
phenyl (4/5 atoms exposed)phenyl (6/6 atoms exposed)aliphatic chain/group (1 atom exposed)
| Final rank | 3.553 | Score | -24.871 |
|---|---|---|---|
| Inter norm | -0.894 | Intra norm | -0.027 |
| Top1000 | no | Excluded | no |
| Contacts | 17 | H-bonds | 12 |
| Artifact reason | geometry warning; 7 clashes; 1 protein clash; moderate strain Δ 23.8 | ||
| Residues |
ARG141
ASN103
HIS102
MET98
TYR94
ARG113
ASP10
ASP45
CYS69
GLY70
GLY72
GLY74
HIS11
PRO12
SER71
TYR46
VAL44
| ||
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 | 11 | Native recall | 0.79 |
| Jaccard | 0.55 | RMSD | - |
| HB strict | 4 | Strict recall | 0.33 |
| HB same residue+role | 3 | HB role recall | 0.33 |
| HB same residue | 3 | HB residue recall | 0.38 |
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
All stored poses for this docking hit
| Pose | Final rank | Inter norm | Score | HB | CT | CT overlap | CT recall | HB role rec. | RMSD | Excluded | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 48 | -0.030515709128067177 | -1.19877 | -34.747 | 2 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 44 | 1.6895562317880846 | -1.04603 | -29.2926 | 5 | 17 | 0 | 0.00 | 0.00 | - | no | Open |
| 40 | 1.9507185505028426 | -0.979011 | -26.2128 | 4 | 20 | 0 | 0.00 | 0.00 | - | no | Open |
| 55 | 2.0459669774127516 | -1.02625 | -26.334 | 6 | 17 | 0 | 0.00 | 0.00 | - | no | Open |
| 47 | 2.5025793028420766 | -0.832971 | -22.4124 | 6 | 9 | 0 | 0.00 | 0.00 | - | no | Open |
| 45 | 3.027762445054875 | -0.971648 | -24.2602 | 5 | 20 | 0 | 0.00 | 0.00 | - | no | Open |
| 29 | 3.5528368927609004 | -0.893906 | -24.8711 | 12 | 17 | 11 | 0.79 | 0.33 | - | no | Current |
Molecular metrics
RDKit SASA burial, strain energy (MMFF94s), ligand efficiency and fit quality for this docking pose.
Scoring & efficiency
Docking score
-24.871kcal/mol
Ligand efficiency (LE)
-0.9212kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-8.594
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
27HA
Physicochemical properties
Molecular weight
430.3Da
Lipinski: ≤ 500 Da
LogP (cLogP)
2.31
Lipinski: ≤ 5
Rotatable bonds
6
Conformational strain (MMFF94s)
Strain energy (ΔE)
23.83kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
130.82kcal/mol
Minimised FF energy
106.99kcal/mol
SASA & burial
✓ computed
SASA (unbound)
602.0Ų
Total solvent-accessible surface area of free ligand
BSA total
480.6Ų
Buried surface area upon binding
BSA apolar
355.9Ų
Hydrophobic contacts buried
BSA polar
124.7Ų
Polar contacts buried
Fraction buried
79.8%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
74.1%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-2144.6Ų
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
812.0Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)