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
34.5 kcal/mol
Protein clashes
3
Internal clashes
3
Native overlap
contact recall 0.86, Jaccard 0.60, H-bond role recall 0.67
Reason: no major geometry red flags detected
3 protein-contact clashes
3 intramolecular clashes
65% of hydrophobic surface is solvent-exposed (17/26 atoms). Large non-polar area without protein contacts incurs a desolvation penalty and will reduce binding affinity. Consider truncating or replacing the exposed fragment.
Molecular report
Weak
Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-0.608 kcal/mol/HA)
✓ Good fit quality (FQ -6.18)
✓ Strong H-bond network (13 bonds)
✓ Deep burial (73% SASA buried)
✓ Lipophilic contacts well-matched (73%)
✗ Very high strain energy (34.5 kcal/mol)
✗ Geometry warnings
✗ Many internal clashes (18)
Score
-21.887
kcal/mol
LE
-0.608
kcal/mol/HA
Fit Quality
-6.18
FQ (Leeson)
HAC
36
heavy atoms
MW
484
Da
LogP
2.11
cLogP
Interaction summary
HB 13
HY 3
PI 1
CLASH 3
⚠ Exposure 65%
Interaction summary
HB 13
HY 3
PI 1
CLASH 3
⚠ Exposure 65%
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
Solvent-exposed hydrophobic surface — desolvation penalty likely
65% of hydrophobic surface is solvent-exposed (17/26 atoms). Large non-polar area without protein contacts incurs a desolvation penalty and will reduce binding affinity. Consider truncating or replacing the exposed fragment.
Non-polar atoms 26
Buried (contacted) 9
Exposed 17
LogP 2.11
H-bonds 13
Exposed fragments:
phenyl (4/5 atoms exposed)phenyl (6/6 atoms exposed)phenyl (5/6 atoms exposed)aliphatic chain/group (4 atoms exposed)
| Final rank | 3.889 | Score | -21.887 |
|---|---|---|---|
| Inter norm | -0.763 | Intra norm | 0.155 |
| Top1000 | no | Excluded | no |
| Contacts | 18 | H-bonds | 13 |
| Artifact reason | geometry warning; 18 clashes; 1 protein clash; high strain Δ 32.2 | ||
| Residues |
ARG137
ARG140
ARG141
ASN103
HIS102
HIS138
MET98
TYR94
ARG113
CYS69
GLY70
GLY72
GLY74
HIS11
ILE73
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 | 0.60 | RMSD | - |
| HB strict | 9 | Strict recall | 0.75 |
| HB same residue+role | 6 | HB role recall | 0.67 |
| HB same residue | 6 | HB residue recall | 0.75 |
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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 22 | 1.3140367446725727 | -0.804232 | -26.1341 | 3 | 20 | 0 | 0.00 | 0.00 | - | no | Open |
| 27 | 1.5349452071704826 | -0.772957 | -24.971 | 3 | 20 | 0 | 0.00 | 0.00 | - | no | Open |
| 31 | 2.9321144294495363 | -0.942471 | -29.4576 | 7 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 13 | 3.8886696484394063 | -0.762846 | -21.8866 | 13 | 18 | 12 | 0.86 | 0.67 | - | no | Current |
| 17 | 4.054842883664916 | -0.618121 | -17.5086 | 4 | 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
-21.887kcal/mol
Ligand efficiency (LE)
-0.6080kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-6.179
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
36HA
Physicochemical properties
Molecular weight
484.5Da
Lipinski: ≤ 500 Da
LogP (cLogP)
2.11
Lipinski: ≤ 5
Rotatable bonds
8
Conformational strain (MMFF94s)
Strain energy (ΔE)
34.54kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
178.25kcal/mol
Minimised FF energy
143.71kcal/mol
SASA & burial
✓ computed
SASA (unbound)
743.2Ų
Total solvent-accessible surface area of free ligand
BSA total
541.9Ų
Buried surface area upon binding
BSA apolar
396.6Ų
Hydrophobic contacts buried
BSA polar
145.3Ų
Polar contacts buried
Fraction buried
72.9%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
73.2%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-2256.7Ų
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
779.7Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)