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
38.0 kcal/mol
Protein clashes
1
Internal clashes
1
Native overlap
contact recall 0.93, Jaccard 0.76, H-bond role recall 0.67
Reason: no major geometry red flags detected
1 protein-contact clashes
68% of hydrophobic surface is solvent-exposed (17/25 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 (-0.679 kcal/mol/HA)
✓ Good fit quality (FQ -6.68)
✓ Strong H-bond network (14 bonds)
✓ Good burial (58% SASA buried)
✓ Lipophilic contacts well-matched (72%)
✗ Very high strain energy (38.0 kcal/mol)
✗ Geometry warnings
✗ Many internal clashes (13)
Score
-21.740
kcal/mol
LE
-0.679
kcal/mol/HA
Fit Quality
-6.68
FQ (Leeson)
HAC
32
heavy atoms
MW
441
Da
LogP
4.21
cLogP
Interaction summary
HB 14
HY 9
PI 2
CLASH 1
⚠ Exposure 68%
Interaction summary
HB 14
HY 9
PI 2
CLASH 1
⚠ Exposure 68%
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
68% of hydrophobic surface is solvent-exposed (17/25 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 25
Buried (contacted) 8
Exposed 17
LogP 4.21
H-bonds 14
Exposed fragments:
phenyl (6/6 atoms exposed)phenyl (4/6 atoms exposed)aliphatic chain/group (9 atoms exposed)
| Final rank | 2.971 | Score | -21.740 |
|---|---|---|---|
| Inter norm | -0.843 | Intra norm | 0.164 |
| Top1000 | no | Excluded | no |
| Contacts | 16 | H-bonds | 14 |
| Artifact reason | geometry warning; 13 clashes; 1 protein clash; moderate strain Δ 29.6 | ||
| Residues |
ARG137
ARG141
ASN103
GLU135
HIS102
MET98
ASP10
CYS69
GLY70
GLY72
GLY74
HIS11
ILE73
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 | 0.76 | RMSD | - |
| HB strict | 7 | Strict recall | 0.58 |
| 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 270 | 1.495655295043211 | -0.906888 | -19.8806 | 5 | 14 | 0 | 0.00 | 0.00 | - | no | Open |
| 202 | 2.6027851694161424 | -0.994833 | -26.7174 | 8 | 25 | 0 | 0.00 | 0.00 | - | no | Open |
| 218 | 2.970827852890614 | -0.842945 | -21.7398 | 14 | 16 | 13 | 0.93 | 0.67 | - | no | Current |
| 245 | 5.3241131212709725 | -0.666612 | -15.7003 | 6 | 10 | 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
-21.740kcal/mol
Ligand efficiency (LE)
-0.6794kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-6.681
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
32HA
Physicochemical properties
Molecular weight
440.5Da
Lipinski: ≤ 500 Da
LogP (cLogP)
4.21
Lipinski: ≤ 5
Rotatable bonds
11
Conformational strain (MMFF94s)
Strain energy (ΔE)
37.97kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
135.03kcal/mol
Minimised FF energy
97.07kcal/mol
SASA & burial
✓ computed
SASA (unbound)
764.6Ų
Total solvent-accessible surface area of free ligand
BSA total
443.9Ų
Buried surface area upon binding
BSA apolar
321.8Ų
Hydrophobic contacts buried
BSA polar
122.0Ų
Polar contacts buried
Fraction buried
58.0%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
72.5%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-2351.5Ų
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
767.4Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)