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
Reject
SASA cached
Likely artefact or unreliable pose
Binding strong
Geometry medium
Native strong
SASA done
Strain ΔE
32.0 kcal/mol
Protein clashes
2
Internal clashes
2
Native overlap
contact recall 1.00, Jaccard 0.74, H-bond role recall 0.56
Reason: no major geometry red flags detected
2 protein-contact clashes
71% of hydrophobic surface is solvent-exposed (25/35 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
Reject
Multiple quality flags — this pose should be deprioritised or discarded.
✓ Excellent LE (-0.520 kcal/mol/HA)
✓ Good fit quality (FQ -5.52)
✓ Strong H-bond network (11 bonds)
✓ Good burial (61% SASA buried)
✓ Lipophilic contacts well-matched (79%)
✗ Very high strain energy (32.0 kcal/mol)
✗ Geometry warnings
✗ Protein-contact clashes (8)
✗ Many internal clashes (20)
Score
-22.344
kcal/mol
LE
-0.520
kcal/mol/HA
Fit Quality
-5.52
FQ (Leeson)
HAC
43
heavy atoms
MW
577
Da
LogP
6.54
cLogP
Interaction summary
HB 11
HY 9
PI 3
CLASH 2
⚠ Exposure 71%
Interaction summary
HB 11
HY 9
PI 3
CLASH 2
⚠ Exposure 71%
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
71% of hydrophobic surface is solvent-exposed (25/35 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 35
Buried (contacted) 10
Exposed 25
LogP 6.54
H-bonds 11
Exposed fragments:
phenyl (6/6 atoms exposed)phenyl (6/6 atoms exposed)phenyl (4/6 atoms exposed)phenyl (6/6 atoms exposed)aliphatic chain/group (5 atoms exposed)
| Final rank | 2.958 | Score | -22.344 |
|---|---|---|---|
| Inter norm | -0.561 | Intra norm | 0.042 |
| Top1000 | no | Excluded | no |
| Contacts | 19 | H-bonds | 11 |
| Artifact reason | geometry warning; 20 clashes; 8 protein contact clashes; moderate strain Δ 29.5 | ||
| Residues |
ARG137
ARG141
ASN103
GLU135
HIS102
HIS138
MET98
ARG113
ASP10
CYS69
GLY70
GLY72
GLY74
HIS11
ILE73
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 | 14 | Native recall | 1.00 |
| Jaccard | 0.74 | RMSD | - |
| HB strict | 5 | Strict recall | 0.42 |
| HB same residue+role | 5 | HB role recall | 0.56 |
| 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 237 | 2.1421301834227364 | -0.701501 | -28.81 | 11 | 14 | 0 | 0.00 | 0.00 | - | no | Open |
| 228 | 2.957704255063165 | -0.561153 | -22.3442 | 11 | 19 | 14 | 1.00 | 0.56 | - | no | Current |
| 370 | 3.1171011997186038 | -0.584444 | -23.6807 | 4 | 13 | 0 | 0.00 | 0.00 | - | no | Open |
| 187 | 3.6334780697999856 | -0.684482 | -23.0287 | 8 | 21 | 0 | 0.00 | 0.00 | - | no | Open |
| 261 | 4.63481545208983 | -0.750261 | -27.7571 | 11 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 172 | 6.106050121218517 | -0.608691 | -21.2125 | 15 | 20 | 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
-22.344kcal/mol
Ligand efficiency (LE)
-0.5196kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-5.523
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
43HA
Physicochemical properties
Molecular weight
576.7Da
Lipinski: ≤ 500 Da
LogP (cLogP)
6.54
Lipinski: ≤ 5
Rotatable bonds
10
Conformational strain (MMFF94s)
Strain energy (ΔE)
31.97kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
150.12kcal/mol
Minimised FF energy
118.15kcal/mol
SASA & burial
✓ computed
SASA (unbound)
913.0Ų
Total solvent-accessible surface area of free ligand
BSA total
555.0Ų
Buried surface area upon binding
BSA apolar
440.4Ų
Hydrophobic contacts buried
BSA polar
114.6Ų
Polar contacts buried
Fraction buried
60.8%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
79.3%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-2454.0Ų
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
812.6Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)