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 medium
Native strong
SASA done
Strain ΔE
18.7 kcal/mol
Protein clashes
3
Internal clashes
3
Native overlap
contact recall 0.93, Jaccard 0.72, H-bond role recall 0.56
Reason: no major geometry red flags detected
3 protein-contact clashes
3 intramolecular clashes
Molecular report
Promising
Reasonable quality metrics. Warrants further investigation.
✓ Excellent LE (-1.083 kcal/mol/HA)
✓ Good fit quality (FQ -9.71)
✓ Strong H-bond network (11 bonds)
✓ Deep burial (86% SASA buried)
✓ Lipophilic contacts well-matched (78%)
✗ Moderate strain (18.7 kcal/mol)
✗ Geometry warnings
✗ Internal clashes (7)
Score
-25.990
kcal/mol
LE
-1.083
kcal/mol/HA
Fit Quality
-9.71
FQ (Leeson)
HAC
24
heavy atoms
MW
324
Da
LogP
3.45
cLogP
Interaction summary
HB 11
HY 7
PI 3
CLASH 3
Interaction summary
HB 11
HY 7
PI 3
CLASH 3
| Final rank | 1.900 | Score | -25.990 |
|---|---|---|---|
| Inter norm | -1.021 | Intra norm | -0.062 |
| Top1000 | no | Excluded | no |
| Contacts | 17 | H-bonds | 11 |
| Artifact reason | geometry warning; 7 clashes; 1 protein clash | ||
| Residues |
ARG137
ARG141
ASN103
HIS102
HIS138
MET98
TYR94
ARG113
ASP10
CYS69
GLY70
GLY72
GLY74
ILE73
PRO12
SER71
TYR46
| ||
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 | 13 | Native recall | 0.93 |
| Jaccard | 0.72 | RMSD | - |
| HB strict | 6 | Strict recall | 0.50 |
| HB same residue+role | 5 | HB role recall | 0.56 |
| HB same residue | 5 | HB residue recall | 0.62 |
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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 387 | 0.36051882321163314 | -1.34004 | -29.2797 | 9 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 417 | 1.8908796334170939 | -1.35793 | -33.9757 | 10 | 14 | 0 | 0.00 | 0.00 | - | no | Open |
| 435 | 1.9004749194382002 | -1.02058 | -25.9903 | 11 | 17 | 13 | 0.93 | 0.56 | - | no | Current |
| 419 | 2.807878564222623 | -1.0264 | -24.6204 | 7 | 9 | 0 | 0.00 | 0.00 | - | no | Open |
| 403 | 3.0441745044344053 | -1.17278 | -25.3923 | 9 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 401 | 3.272585015045708 | -1.014 | -21.3315 | 7 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 496 | 4.171712409869473 | -0.992234 | -24.6771 | 8 | 13 | 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
-25.990kcal/mol
Ligand efficiency (LE)
-1.0829kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-9.705
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
24HA
Physicochemical properties
Molecular weight
324.3Da
Lipinski: ≤ 500 Da
LogP (cLogP)
3.45
Lipinski: ≤ 5
Rotatable bonds
5
Conformational strain (MMFF94s)
Strain energy (ΔE)
18.68kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
69.68kcal/mol
Minimised FF energy
51.00kcal/mol
SASA & burial
✓ computed
SASA (unbound)
534.1Ų
Total solvent-accessible surface area of free ligand
BSA total
459.4Ų
Buried surface area upon binding
BSA apolar
358.5Ų
Hydrophobic contacts buried
BSA polar
100.9Ų
Polar contacts buried
Fraction buried
86.0%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
78.0%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-2156.8Ų
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
747.5Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)