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
Promising
SASA cached
Promising and worth follow-up
Binding strong
Geometry high
Native strong
SASA done
Strain ΔE
19.8 kcal/mol
Protein clashes
2
Internal clashes
2
Native overlap
contact recall 0.79, Jaccard 0.65, H-bond role recall 0.33
Reason: no major geometry red flags detected
2 protein-contact clashes
Molecular report
Promising
Reasonable quality metrics. Warrants further investigation.
✓ Excellent LE (-0.872 kcal/mol/HA)
✓ Good fit quality (FQ -8.23)
✓ Strong H-bond network (7 bonds)
✓ Deep burial (71% SASA buried)
✓ Lipophilic contacts well-matched (69%)
✗ Moderate strain (19.8 kcal/mol)
✗ Geometry warnings
✗ Internal clashes (8)
Score
-24.403
kcal/mol
LE
-0.872
kcal/mol/HA
Fit Quality
-8.23
FQ (Leeson)
HAC
28
heavy atoms
MW
417
Da
LogP
2.68
cLogP
Interaction summary
HB 7
HY 8
PI 6
CLASH 2
Interaction summary
HB 7
HY 8
PI 6
CLASH 2
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
| Final rank | 2.273 | Score | -24.403 |
|---|---|---|---|
| Inter norm | -0.936 | Intra norm | 0.064 |
| Top1000 | no | Excluded | no |
| Contacts | 14 | H-bonds | 7 |
| Artifact reason | geometry warning; 8 clashes; 1 protein clash | ||
| Residues |
ARG137
ARG141
ASN103
HIS102
HIS138
MET98
TYR94
ARG113
CYS69
GLY70
GLY74
HIS11
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 | 11 | Native recall | 0.79 |
| Jaccard | 0.65 | 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 |
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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 621 | 1.4345497717291078 | -1.0318 | -28.9875 | 10 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 624 | 1.9005361944032626 | -0.963332 | -23.5994 | 3 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 633 | 2.034066149755648 | -0.997448 | -27.4985 | 5 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 614 | 2.1205691892069596 | -1.06766 | -31.8052 | 5 | 10 | 0 | 0.00 | 0.00 | - | no | Open |
| 617 | 2.21543994317517 | -0.943733 | -25.4581 | 5 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 636 | 2.2733624275643116 | -0.935816 | -24.4034 | 7 | 14 | 11 | 0.79 | 0.33 | - | no | Current |
| 631 | 2.613527185358712 | -0.808865 | -21.8381 | 2 | 15 | 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
-24.403kcal/mol
Ligand efficiency (LE)
-0.8716kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-8.228
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
28HA
Physicochemical properties
Molecular weight
416.5Da
Lipinski: ≤ 500 Da
LogP (cLogP)
2.68
Lipinski: ≤ 5
Rotatable bonds
5
Conformational strain (MMFF94s)
Strain energy (ΔE)
19.77kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
23.63kcal/mol
Minimised FF energy
3.86kcal/mol
SASA & burial
✓ computed
SASA (unbound)
640.9Ų
Total solvent-accessible surface area of free ligand
BSA total
453.8Ų
Buried surface area upon binding
BSA apolar
311.6Ų
Hydrophobic contacts buried
BSA polar
142.2Ų
Polar contacts buried
Fraction buried
70.8%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
68.7%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-2202.8Ų
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
742.1Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)