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
19.5 kcal/mol
Protein clashes
3
Internal clashes
3
Native overlap
contact recall 0.93, Jaccard 0.76, H-bond role recall 0.44
Reason: no major geometry red flags detected
3 protein-contact clashes
3 intramolecular clashes
59% of hydrophobic surface appears solvent-exposed (13/22 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 (-0.773 kcal/mol/HA)
✓ Good fit quality (FQ -7.46)
✓ Strong H-bond network (10 bonds)
✓ Deep burial (68% SASA buried)
✓ Lipophilic contacts well-matched (76%)
✗ Moderate strain (19.5 kcal/mol)
✗ Geometry warnings
✗ Many internal clashes (13)
Score
-23.189
kcal/mol
LE
-0.773
kcal/mol/HA
Fit Quality
-7.46
FQ (Leeson)
HAC
30
heavy atoms
MW
429
Da
LogP
4.30
cLogP
Interaction summary
HB 10
HY 9
PI 3
CLASH 3
⚠ Exposure 59%
Interaction summary
HB 10
HY 9
PI 3
CLASH 3
⚠ Exposure 59%
Partial hydrophobic solvent exposure
59% of hydrophobic surface appears solvent-exposed (13/22 atoms). Partial exposure is common but may limit selectivity and membrane permeability.
Non-polar atoms 22
Buried (contacted) 9
Exposed 13
LogP 4.3
H-bonds 10
Exposed fragments:
phenyl (6/6 atoms exposed)phenyl (4/6 atoms exposed)aliphatic chain/group (5 atoms exposed)
| Final rank | 2.944 | Score | -23.189 |
|---|---|---|---|
| Inter norm | -0.930 | Intra norm | 0.157 |
| Top1000 | no | Excluded | no |
| Contacts | 16 | H-bonds | 10 |
| Artifact reason | geometry warning; 13 clashes; 1 protein clash | ||
| Residues |
ARG137
ARG141
ASN103
HIS102
ASP10
CYS69
GLY70
GLY72
GLY74
HIS11
ILE73
MET75
PRO12
SER43
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 | 0.76 | 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 |
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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 275 | 0.7889979072658933 | -0.992564 | -28.8915 | 4 | 18 | 0 | 0.00 | 0.00 | - | no | Open |
| 228 | 1.6816624502728075 | -0.859939 | -20.8455 | 3 | 19 | 0 | 0.00 | 0.00 | - | no | Open |
| 222 | 2.9440354789749033 | -0.929592 | -23.1893 | 10 | 16 | 13 | 0.93 | 0.44 | - | no | Current |
| 222 | 3.169631879952202 | -0.962424 | -26.3287 | 5 | 12 | 0 | 0.00 | 0.00 | - | no | Open |
| 199 | 3.5180411759997106 | -0.930123 | -25.8374 | 6 | 18 | 0 | 0.00 | 0.00 | - | no | Open |
| 165 | 3.5452832882454475 | -1.04133 | -26.5489 | 9 | 21 | 0 | 0.00 | 0.00 | - | no | Open |
| 302 | 3.5505546180031344 | -0.849466 | -26.2435 | 7 | 19 | 0 | 0.00 | 0.00 | - | no | Open |
| 250 | 3.9636286797484552 | -0.719092 | -19.5389 | 5 | 14 | 0 | 0.00 | 0.00 | - | no | Open |
| 167 | 4.1545336271829 | -1.07531 | -27.7999 | 11 | 17 | 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
-23.189kcal/mol
Ligand efficiency (LE)
-0.7730kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-7.456
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
30HA
Physicochemical properties
Molecular weight
428.5Da
Lipinski: ≤ 500 Da
LogP (cLogP)
4.30
Lipinski: ≤ 5
Rotatable bonds
7
Conformational strain (MMFF94s)
Strain energy (ΔE)
19.51kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
94.19kcal/mol
Minimised FF energy
74.68kcal/mol
SASA & burial
✓ computed
SASA (unbound)
701.5Ų
Total solvent-accessible surface area of free ligand
BSA total
479.3Ų
Buried surface area upon binding
BSA apolar
365.9Ų
Hydrophobic contacts buried
BSA polar
113.4Ų
Polar contacts buried
Fraction buried
68.3%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
76.3%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-2284.0Ų
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
758.1Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)