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
23.8 kcal/mol
Protein clashes
4
Internal clashes
4
Native overlap
contact recall 1.00, Jaccard 0.74, H-bond role recall 0.33
Reason: no major geometry red flags detected
4 protein-contact clashes
4 intramolecular clashes
36% of hydrophobic surface appears solvent-exposed (9/25 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 (-0.616 kcal/mol/HA)
✓ Good fit quality (FQ -6.11)
✓ Strong H-bond network (9 bonds)
✓ Deep burial (74% SASA buried)
✓ Lipophilic contacts well-matched (81%)
✗ High strain energy (23.8 kcal/mol)
✗ Geometry warnings
✗ Many internal clashes (15)
Score
-20.334
kcal/mol
LE
-0.616
kcal/mol/HA
Fit Quality
-6.11
FQ (Leeson)
HAC
33
heavy atoms
MW
455
Da
LogP
2.76
cLogP
Interaction summary
HB 9
HY 10
PI 3
CLASH 4
⚠ Exposure 36%
Interaction summary
HB 9
HY 10
PI 3
CLASH 4
⚠ Exposure 36%
Partial hydrophobic solvent exposure
36% of hydrophobic surface appears solvent-exposed (9/25 atoms). Partial exposure is common but may limit selectivity and membrane permeability.
Non-polar atoms 25
Buried (contacted) 16
Exposed 9
LogP 2.76
H-bonds 9
Exposed fragments:
aliphatic chain/group (9 atoms exposed)
| Final rank | 5.229 | Score | -20.334 |
|---|---|---|---|
| Inter norm | -0.827 | Intra norm | 0.211 |
| Top1000 | no | Excluded | no |
| Contacts | 19 | H-bonds | 9 |
| Artifact reason | geometry warning; 15 clashes; 3 protein clashes; moderate strain Δ 23.8 | ||
| Residues |
ARG137
ARG141
ASN103
HIS102
HIS138
MET98
TYR94
ARG113
ASP10
CYS69
GLY70
GLY72
GLY74
HIS11
ILE73
MET75
PRO12
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 | 14 | Native recall | 1.00 |
| Jaccard | 0.74 | RMSD | - |
| HB strict | 3 | Strict recall | 0.25 |
| HB same residue+role | 3 | HB role recall | 0.33 |
| HB same residue | 4 | HB residue recall | 0.50 |
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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 296 | 1.2094497069229952 | -0.798718 | -24.0361 | 4 | 19 | 0 | 0.00 | 0.00 | - | no | Open |
| 246 | 1.5777109956035995 | -1.02348 | -27.0051 | 6 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 217 | 2.907166553436376 | -0.828931 | -26.0142 | 6 | 18 | 0 | 0.00 | 0.00 | - | no | Open |
| 272 | 2.937604839504376 | -0.709141 | -16.628 | 8 | 14 | 0 | 0.00 | 0.00 | - | no | Open |
| 264 | 3.3766176770969594 | -0.963848 | -30.2461 | 8 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 195 | 3.764082353800593 | -0.885488 | -30.0305 | 8 | 20 | 0 | 0.00 | 0.00 | - | no | Open |
| 253 | 5.228683162267013 | -0.827143 | -20.3337 | 9 | 19 | 14 | 1.00 | 0.33 | - | no | Current |
| 235 | 5.457047523773753 | -0.802528 | -20.4234 | 6 | 18 | 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
-20.334kcal/mol
Ligand efficiency (LE)
-0.6162kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-6.114
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
33HA
Physicochemical properties
Molecular weight
454.5Da
Lipinski: ≤ 500 Da
LogP (cLogP)
2.76
Lipinski: ≤ 5
Rotatable bonds
9
Conformational strain (MMFF94s)
Strain energy (ΔE)
23.82kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
55.68kcal/mol
Minimised FF energy
31.86kcal/mol
SASA & burial
✓ computed
SASA (unbound)
738.3Ų
Total solvent-accessible surface area of free ligand
BSA total
550.3Ų
Buried surface area upon binding
BSA apolar
443.6Ų
Hydrophobic contacts buried
BSA polar
106.8Ų
Polar contacts buried
Fraction buried
74.5%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
80.6%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-2326.2Ų
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
748.8Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)