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
59.5 kcal/mol
Protein clashes
5
Internal clashes
5
Native overlap
contact recall 0.93, Jaccard 0.68, H-bond role recall 0.78
Reason: strain 59.5 kcal/mol
strain ΔE 59.5 kcal/mol
5 protein-contact clashes
5 intramolecular clashes
42% of hydrophobic surface appears solvent-exposed (5/12 atoms). Partial exposure is common but may limit selectivity and membrane permeability.
Molecular report
Reject
Multiple quality flags — this pose should be deprioritised or discarded.
✓ Excellent LE (-0.735 kcal/mol/HA)
✓ Good fit quality (FQ -6.77)
✓ Strong H-bond network (8 bonds)
✓ Deep burial (86% SASA buried)
✗ Extreme strain energy (59.5 kcal/mol)
✗ Geometry warnings
✗ Internal clashes (5)
Score
-19.097
kcal/mol
LE
-0.735
kcal/mol/HA
Fit Quality
-6.77
FQ (Leeson)
HAC
26
heavy atoms
MW
393
Da
LogP
-2.41
cLogP
Final rank
3.8810
rank score
Inter norm
-1.029
normalised
Contacts
18
H-bonds 16
Interaction summary
HBD 1
HBA 7
HY 2
PI 1
CLASH 5
Interaction summary
HBD 1
HBA 7
HY 2
PI 1
CLASH 5
HBD/HBA · H-bonds (geometric)
HBD = ligand donates H · HBA = ligand accepts H · ~ = weak (≥110°). Mode: strict. Residues: 5.
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: 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 | 9 | Strict recall | 0.75 |
| HB same residue+role | 7 | HB role recall | 0.78 |
| HB same residue | 6 | HB residue recall | 0.75 |
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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 40 | 0.7855830598338656 | -1.24651 | -24.0164 | 5 | 10 | 0 | 0.00 | 0.00 | - | no | Open |
| 39 | 3.881012812911613 | -1.02877 | -19.097 | 16 | 18 | 13 | 0.93 | 0.78 | - | no | Current |
| 62 | 4.044692383763179 | -1.52646 | -33.64 | 14 | 19 | 0 | 0.00 | 0.00 | - | no | Open |
| 73 | 4.3547764325944724 | -1.10988 | -24.1849 | 14 | 20 | 0 | 0.00 | 0.00 | - | no | Open |
| 46 | 5.49749655784152 | -0.910738 | -20.4574 | 10 | 14 | 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
-19.097kcal/mol
Ligand efficiency (LE)
-0.7345kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-6.767
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
26HA
Physicochemical properties
Molecular weight
393.3Da
Lipinski: ≤ 500 Da
LogP (cLogP)
-2.41
Lipinski: ≤ 5
Rotatable bonds
13
Conformational strain (MMFF94s)
Strain energy (ΔE)
59.46kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
67.22kcal/mol
Minimised FF energy
7.76kcal/mol
SASA & burial
✓ computed
SASA (unbound)
557.1Ų
Total solvent-accessible surface area of free ligand
BSA total
480.5Ų
Buried surface area upon binding
BSA apolar
287.7Ų
Hydrophobic contacts buried
BSA polar
192.8Ų
Polar contacts buried
Fraction buried
86.2%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
59.9%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-2079.6Ų
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
732.2Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)