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
Promising but geometrically suspicious
Binding strong
Geometry low
Native strong
SASA done
Strain ΔE
24.3 kcal/mol
Protein clashes
0
Internal clashes
11
Native overlap
contact recall 0.93, Jaccard 0.81, H-bond role recall 0.33
Reason: 11 internal clashes
11 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
Weak
Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-0.801 kcal/mol/HA)
✓ Good fit quality (FQ -7.57)
✓ Strong H-bond network (9 bonds)
✓ Deep burial (74% SASA buried)
✓ Lipophilic contacts well-matched (82%)
✗ High strain energy (24.3 kcal/mol)
✗ Geometry warnings
✗ Many internal clashes (11)
Score
-22.438
kcal/mol
LE
-0.801
kcal/mol/HA
Fit Quality
-7.57
FQ (Leeson)
HAC
28
heavy atoms
MW
374
Da
LogP
3.28
cLogP
Interaction summary
HB 9
HY 6
PI 2
CLASH 0
⚠ Exposure 35%
Interaction summary
HB 9
HY 6
PI 2
CLASH 0
⚠ 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
No clash · clashes detected for this pose.
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 3.28
H-bonds 9
Exposed fragments:
phenyl (4/6 atoms exposed)phenyl (3/5 atoms exposed)aliphatic chain/group (2 atoms exposed)
| Final rank | 3.273 | Score | -22.438 |
|---|---|---|---|
| Inter norm | -0.915 | Intra norm | 0.113 |
| Top1000 | no | Excluded | no |
| Contacts | 15 | H-bonds | 9 |
| Artifact reason | geometry warning; 11 clashes; 2 protein clashes; moderate strain Δ 24.3 | ||
| Residues |
ARG137
ARG141
ASN103
HIS102
HIS138
ALA41
ARG113
ASP10
CYS69
GLY70
GLY74
HIS11
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 | 13 | Native recall | 0.93 |
| Jaccard | 0.81 | RMSD | - |
| HB strict | 4 | Strict recall | 0.33 |
| HB same residue+role | 3 | HB role recall | 0.33 |
| 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 426 | 0.20770404577612916 | -1.13873 | -25.8264 | 7 | 18 | 0 | 0.00 | 0.00 | - | no | Open |
| 420 | 1.6818039381286587 | -1.20032 | -26.424 | 8 | 20 | 0 | 0.00 | 0.00 | - | no | Open |
| 455 | 2.477135703355753 | -1.11435 | -27.8624 | 7 | 18 | 0 | 0.00 | 0.00 | - | no | Open |
| 455 | 2.8965566461410885 | -0.813135 | -21.8999 | 4 | 13 | 0 | 0.00 | 0.00 | - | no | Open |
| 464 | 3.27287170032687 | -0.914601 | -22.4375 | 9 | 15 | 13 | 0.93 | 0.33 | - | no | Current |
| 410 | 3.374781699121479 | -1.05774 | -25.0914 | 8 | 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
-22.438kcal/mol
Ligand efficiency (LE)
-0.8013kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-7.565
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
28HA
Physicochemical properties
Molecular weight
374.4Da
Lipinski: ≤ 500 Da
LogP (cLogP)
3.28
Lipinski: ≤ 5
Rotatable bonds
6
Conformational strain (MMFF94s)
Strain energy (ΔE)
24.31kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
99.84kcal/mol
Minimised FF energy
75.53kcal/mol
SASA & burial
✓ computed
SASA (unbound)
637.5Ų
Total solvent-accessible surface area of free ligand
BSA total
474.1Ų
Buried surface area upon binding
BSA apolar
390.9Ų
Hydrophobic contacts buried
BSA polar
83.2Ų
Polar contacts buried
Fraction buried
74.4%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
82.4%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-2246.2Ų
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
782.1Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)