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
Reject
SASA cached
Promising but geometrically suspicious
Binding strong
Geometry low
Native strong
SASA done
Strain ΔE
55.2 kcal/mol
Protein clashes
4
Internal clashes
4
Native overlap
contact recall 0.93, Jaccard 0.68, H-bond role recall 0.33
Reason: strain 55.2 kcal/mol
strain ΔE 55.2 kcal/mol
4 protein-contact clashes
4 intramolecular clashes
70% of hydrophobic surface is solvent-exposed (19/27 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
Reject
Multiple quality flags — this pose should be deprioritised or discarded.
✓ Excellent LE (-0.541 kcal/mol/HA)
✓ Good fit quality (FQ -5.50)
✓ Good H-bonds (5 bonds)
✓ Deep burial (72% SASA buried)
✓ Lipophilic contacts well-matched (79%)
✗ Extreme strain energy (55.2 kcal/mol)
✗ Geometry warnings
✗ Many internal clashes (12)
Score
-19.462
kcal/mol
LE
-0.541
kcal/mol/HA
Fit Quality
-5.50
FQ (Leeson)
HAC
36
heavy atoms
MW
499
Da
LogP
1.32
cLogP
Final rank
4.8564
rank score
Inter norm
-0.731
normalised
Contacts
18
H-bonds 9
Interaction summary
HBD 2
HBA 3
HY 4
PI 2
CLASH 4
Interaction summary
HBD 2
HBA 3
HY 4
PI 2
CLASH 4
HBD/HBA · H-bonds (geometric)
HBD = ligand donates H · HBA = ligand accepts H · ~ = weak (≥110°). Mode: permissive. Residues: 4.
PI · π–π interactions
Native π–π recall is disabled because no explicit native π–π reference was stored.
HY · Hydrophobic contacts
CLASH · Clashes
Native ligand reference
★ reference
Interaction fingerprint calculated directly from the uploaded native ligand without docking. Current H-bond mode: permissive.
| 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 | 3 | Strict recall | 0.25 |
| HB same residue+role | 3 | HB role recall | 0.33 |
| 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 297 | 0.7133550270525915 | -0.900154 | -28.1429 | 2 | 21 | 0 | 0.00 | 0.00 | - | no | Open |
| 247 | 0.8841488795399569 | -1.05271 | -26.0105 | 4 | 17 | 0 | 0.00 | 0.00 | - | no | Open |
| 293 | 3.831697810407351 | -0.521837 | -15.2673 | 6 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 254 | 4.856409708403751 | -0.731116 | -19.4621 | 9 | 18 | 13 | 0.93 | 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
-19.462kcal/mol
Ligand efficiency (LE)
-0.5406kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-5.495
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
36HA
Physicochemical properties
Molecular weight
498.6Da
Lipinski: ≤ 500 Da
LogP (cLogP)
1.32
Lipinski: ≤ 5
Rotatable bonds
11
Conformational strain (MMFF94s)
Strain energy (ΔE)
55.19kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
82.68kcal/mol
Minimised FF energy
27.48kcal/mol
SASA & burial
✓ computed
SASA (unbound)
723.8Ų
Total solvent-accessible surface area of free ligand
BSA total
518.2Ų
Buried surface area upon binding
BSA apolar
407.2Ų
Hydrophobic contacts buried
BSA polar
111.0Ų
Polar contacts buried
Fraction buried
71.6%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
78.6%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-2323.9Ų
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
745.5Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)