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
Reject
SASA cached
Promising but geometrically suspicious
Binding strong
Geometry low
Native strong
SASA done
Strain ΔE
51.1 kcal/mol
Protein clashes
3
Internal clashes
3
Native overlap
contact recall 0.86, Jaccard 0.63, H-bond role recall 0.67
Reason: strain 51.1 kcal/mol
strain ΔE 51.1 kcal/mol
3 protein-contact clashes
3 intramolecular clashes
35% of hydrophobic surface appears solvent-exposed (7/20 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 (-0.851 kcal/mol/HA)
✓ Good fit quality (FQ -8.29)
✓ Strong H-bond network (10 bonds)
✓ Deep burial (68% SASA buried)
✓ Lipophilic contacts well-matched (62%)
✗ Extreme strain energy (51.1 kcal/mol)
✗ Geometry warnings
✗ Many internal clashes (16)
Score
-26.378
kcal/mol
LE
-0.851
kcal/mol/HA
Fit Quality
-8.29
FQ (Leeson)
HAC
31
heavy atoms
MW
454
Da
LogP
2.74
cLogP
Interaction summary
HB 10
HY 5
PI 4
CLASH 3
⚠ Exposure 35%
Interaction summary
HB 10
HY 5
PI 4
CLASH 3
⚠ Exposure 35%
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
Partial hydrophobic solvent exposure
35% of hydrophobic surface appears solvent-exposed (7/20 atoms). Partial exposure is common but may limit selectivity and membrane permeability.
Non-polar atoms 20
Buried (contacted) 13
Exposed 7
LogP 2.74
H-bonds 10
Exposed fragments:
phenyl (6/6 atoms exposed)aliphatic chain/group (1 atom exposed)
| Final rank | 3.563 | Score | -26.378 |
|---|---|---|---|
| Inter norm | -0.826 | Intra norm | -0.024 |
| Top1000 | no | Excluded | no |
| Contacts | 17 | H-bonds | 10 |
| Artifact reason | geometry warning; 16 clashes; 1 protein clash; high strain Δ 51.1 | ||
| Residues |
ARG137
ARG141
ASN103
HIS102
HIS138
MET98
TYR94
ARG113
CYS69
GLY70
GLY72
GLY74
HIS11
PRO12
SER43
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 | 0.63 | RMSD | - |
| HB strict | 7 | Strict recall | 0.58 |
| HB same residue+role | 6 | HB role recall | 0.67 |
| 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 513 | 1.6936180047675053 | -0.79421 | -25.1545 | 4 | 18 | 0 | 0.00 | 0.00 | - | no | Open |
| 524 | 2.3042851226977157 | -0.627989 | -26.8406 | 7 | 11 | 0 | 0.00 | 0.00 | - | no | Open |
| 536 | 3.563455666719602 | -0.826478 | -26.3784 | 10 | 17 | 12 | 0.86 | 0.67 | - | no | Current |
| 517 | 3.8753577557480097 | -0.889061 | -32.2082 | 9 | 19 | 0 | 0.00 | 0.00 | - | no | Open |
| 509 | 3.9625485656986896 | -0.944851 | -31.682 | 10 | 16 | 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
-26.378kcal/mol
Ligand efficiency (LE)
-0.8509kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-8.290
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
31HA
Physicochemical properties
Molecular weight
453.5Da
Lipinski: ≤ 500 Da
LogP (cLogP)
2.74
Lipinski: ≤ 5
Rotatable bonds
6
Conformational strain (MMFF94s)
Strain energy (ΔE)
51.09kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
19.50kcal/mol
Minimised FF energy
-31.59kcal/mol
SASA & burial
✓ computed
SASA (unbound)
701.9Ų
Total solvent-accessible surface area of free ligand
BSA total
479.1Ų
Buried surface area upon binding
BSA apolar
294.4Ų
Hydrophobic contacts buried
BSA polar
184.7Ų
Polar contacts buried
Fraction buried
68.3%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
61.5%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-2187.3Ų
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
786.1Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)