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
Promising
SASA cached
Promising and worth follow-up
Binding strong
Geometry high
Native strong
SASA done
Strain ΔE
7.3 kcal/mol
Protein clashes
1
Internal clashes
1
Native overlap
contact recall 1.00, Jaccard 0.74, H-bond role recall 0.33
Reason: no major geometry red flags detected
1 protein-contact clashes
Molecular report
Promising
Reasonable quality metrics. Warrants further investigation.
✓ Low conformational strain (7.3 kcal/mol)
✓ Excellent LE (-1.258 kcal/mol/HA)
✓ Good fit quality (FQ -10.73)
✓ Good H-bonds (4 bonds)
✓ Deep burial (86% SASA buried)
✓ Lipophilic contacts well-matched (97%)
✗ Geometry warnings
✗ Internal clashes (7)
Score
-26.427
kcal/mol
LE
-1.258
kcal/mol/HA
Fit Quality
-10.73
FQ (Leeson)
HAC
21
heavy atoms
MW
276
Da
LogP
3.02
cLogP
Interaction summary
HB 4
HY 7
PI 3
CLASH 1
Interaction summary
HB 4
HY 7
PI 3
CLASH 1
| Final rank | 2.615 | Score | -26.427 |
|---|---|---|---|
| Inter norm | -1.311 | Intra norm | 0.052 |
| Top1000 | no | Excluded | no |
| Contacts | 19 | H-bonds | 4 |
| Artifact reason | geometry warning; 7 clashes; 2 protein clashes | ||
| Residues |
ARG137
ARG141
ASN103
HIS102
HIS138
MET98
TYR94
ARG113
ASP10
ASP45
CYS69
GLY70
GLY72
GLY74
HIS11
ILE73
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 | 2 | HB residue recall | 0.25 |
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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 661 | 1.3301225924586448 | -1.53409 | -29.212 | 3 | 14 | 0 | 0.00 | 0.00 | - | no | Open |
| 669 | 1.5700738045781129 | -1.13597 | -17.9714 | 6 | 17 | 0 | 0.00 | 0.00 | - | no | Open |
| 657 | 1.577400629558791 | -1.10426 | -22.553 | 5 | 11 | 0 | 0.00 | 0.00 | - | no | Open |
| 675 | 2.2225127768025614 | -0.945388 | -20.0759 | 4 | 11 | 0 | 0.00 | 0.00 | - | no | Open |
| 676 | 2.614827992980293 | -1.31059 | -26.4268 | 4 | 19 | 14 | 1.00 | 0.33 | - | no | Current |
Molecular metrics
RDKit SASA burial, strain energy (MMFF94s), ligand efficiency and fit quality for this docking pose.
Scoring & efficiency
Docking score
-26.427kcal/mol
Ligand efficiency (LE)
-1.2584kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-10.734
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
21HA
Physicochemical properties
Molecular weight
276.4Da
Lipinski: ≤ 500 Da
LogP (cLogP)
3.02
Lipinski: ≤ 5
Rotatable bonds
4
Conformational strain (MMFF94s)
Strain energy (ΔE)
7.33kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
54.93kcal/mol
Minimised FF energy
47.60kcal/mol
SASA & burial
✓ computed
SASA (unbound)
512.5Ų
Total solvent-accessible surface area of free ligand
BSA total
438.3Ų
Buried surface area upon binding
BSA apolar
423.4Ų
Hydrophobic contacts buried
BSA polar
14.9Ų
Polar contacts buried
Fraction buried
85.5%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
96.6%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-2229.4Ų
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
750.2Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)