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
Weak
SASA cached
Weak or marginal quality
Binding strong
Geometry medium
Native strong
SASA done
Strain ΔE
33.8 kcal/mol
Protein clashes
1
Internal clashes
1
Native overlap
contact recall 0.86, Jaccard 0.67, H-bond role recall 0.56
Reason: no major geometry red flags detected
1 protein-contact clashes
60% of hydrophobic surface is solvent-exposed (9/15 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 (-0.827 kcal/mol/HA)
✓ Good fit quality (FQ -7.62)
✓ Strong H-bond network (6 bonds)
✓ Deep burial (70% SASA buried)
✓ Lipophilic contacts well-matched (64%)
✗ Very high strain energy (33.8 kcal/mol)
✗ Geometry warnings
✗ Internal clashes (8)
Score
-21.498
kcal/mol
LE
-0.827
kcal/mol/HA
Fit Quality
-7.62
FQ (Leeson)
HAC
26
heavy atoms
MW
418
Da
LogP
0.61
cLogP
Final rank
4.4967
rank score
Inter norm
-0.956
normalised
Contacts
16
H-bonds 11
Interaction summary
HBD 2
HBA 4
HY 1
PI 1
CLASH 1
Interaction summary
HBD 2
HBA 4
HY 1
PI 1
CLASH 1
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 | 12 | Native recall | 0.86 |
| Jaccard | 0.67 | RMSD | - |
| HB strict | 6 | Strict recall | 0.50 |
| HB same residue+role | 5 | HB role recall | 0.56 |
| 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 561 | 1.281315128434903 | -1.16481 | -29.2191 | 3 | 17 | 0 | 0.00 | 0.00 | - | no | Open |
| 599 | 1.9617089119884996 | -0.797676 | -21.4203 | 7 | 13 | 0 | 0.00 | 0.00 | - | no | Open |
| 590 | 3.519689719153305 | -0.991228 | -22.6292 | 5 | 19 | 0 | 0.00 | 0.00 | - | no | Open |
| 570 | 3.6491157227042055 | -0.996974 | -24.9528 | 4 | 20 | 0 | 0.00 | 0.00 | - | no | Open |
| 566 | 4.1449485637692485 | -1.11173 | -25.5792 | 12 | 17 | 0 | 0.00 | 0.00 | - | no | Open |
| 581 | 4.392249020894027 | -0.932022 | -23.6087 | 14 | 17 | 0 | 0.00 | 0.00 | - | no | Open |
| 597 | 4.496744275640383 | -0.955549 | -21.4979 | 11 | 16 | 12 | 0.86 | 0.56 | - | no | Current |
| 594 | 5.62570554899604 | -1.46712 | -38.3289 | 11 | 23 | 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
-21.498kcal/mol
Ligand efficiency (LE)
-0.8268kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-7.618
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
26HA
Physicochemical properties
Molecular weight
417.9Da
Lipinski: ≤ 500 Da
LogP (cLogP)
0.61
Lipinski: ≤ 5
Rotatable bonds
8
Conformational strain (MMFF94s)
Strain energy (ΔE)
33.77kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
-166.47kcal/mol
Minimised FF energy
-200.24kcal/mol
SASA & burial
✓ computed
SASA (unbound)
650.8Ų
Total solvent-accessible surface area of free ligand
BSA total
458.4Ų
Buried surface area upon binding
BSA apolar
293.1Ų
Hydrophobic contacts buried
BSA polar
165.3Ų
Polar contacts buried
Fraction buried
70.4%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
63.9%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-2125.7Ų
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
797.1Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)