Molecular metrics status: done
RDKit SASA-based burial metrics are cached.
SASA cached
3D complex viewer
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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
26.5 kcal/mol
Protein clashes
3
Internal clashes
3
Native overlap
contact recall 0.86, Jaccard 0.71, H-bond role recall 0.44
Reason: no major geometry red flags detected
3 protein-contact clashes
3 intramolecular clashes
Molecular report
Weak
Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-1.003 kcal/mol/HA)
✓ Good fit quality (FQ -8.85)
✓ Strong H-bond network (8 bonds)
✓ Deep burial (80% SASA buried)
✓ Lipophilic contacts well-matched (74%)
✗ High strain energy (26.5 kcal/mol)
✗ Geometry warnings
✗ Many internal clashes (13)
Score
-23.063
kcal/mol
LE
-1.003
kcal/mol/HA
Fit Quality
-8.85
FQ (Leeson)
HAC
23
heavy atoms
MW
311
Da
LogP
1.70
cLogP
Interaction summary
HB 8
HY 12
PI 3
CLASH 3
Interaction summary
HB 8
HY 12
PI 3
CLASH 3
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 | 3.291 | Score | -23.063 |
|---|---|---|---|
| Inter norm | -1.180 | Intra norm | 0.177 |
| Top1000 | no | Excluded | no |
| Contacts | 15 | H-bonds | 8 |
| Artifact reason | geometry warning; 13 clashes; 2 protein clashes; moderate strain Δ 26.5 | ||
| Residues |
ARG141
ASN103
HIS102
ARG113
ASP10
CYS69
GLY70
GLY72
GLY74
HIS11
ILE73
MET75
PRO12
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 | 12 | Native recall | 0.86 |
| Jaccard | 0.71 | RMSD | - |
| HB strict | 4 | Strict recall | 0.33 |
| HB same residue+role | 4 | HB role recall | 0.44 |
| HB same residue | 5 | HB residue recall | 0.62 |
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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 647 | 3.034867028131142 | -1.52382 | -26.7145 | 10 | 17 | 0 | 0.00 | 0.00 | - | no | Open |
| 650 | 3.291496188177528 | -1.17975 | -23.0628 | 8 | 15 | 12 | 0.86 | 0.44 | - | no | Current |
| 634 | 4.038440949088263 | -1.19467 | -24.7538 | 8 | 12 | 0 | 0.00 | 0.00 | - | no | Open |
| 648 | 4.301744094529095 | -1.14839 | -23.4369 | 14 | 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
-23.063kcal/mol
Ligand efficiency (LE)
-1.0027kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-8.850
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
23HA
Physicochemical properties
Molecular weight
311.3Da
Lipinski: ≤ 500 Da
LogP (cLogP)
1.70
Lipinski: ≤ 5
Rotatable bonds
5
Conformational strain (MMFF94s)
Strain energy (ΔE)
26.55kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
93.53kcal/mol
Minimised FF energy
66.98kcal/mol
SASA & burial
✓ computed
SASA (unbound)
532.6Ų
Total solvent-accessible surface area of free ligand
BSA total
425.2Ų
Buried surface area upon binding
BSA apolar
314.8Ų
Hydrophobic contacts buried
BSA polar
110.5Ų
Polar contacts buried
Fraction buried
79.8%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
74.0%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-2120.1Ų
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
775.7Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)