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 medium
Native strong
SASA done
Strain ΔE
9.7 kcal/mol
Protein clashes
5
Internal clashes
5
Native overlap
contact recall 0.71, Jaccard 0.53, H-bond role recall 0.33
Reason: no major geometry red flags detected
5 protein-contact clashes
5 intramolecular clashes
Molecular report
Promising
Reasonable quality metrics. Warrants further investigation.
✓ Excellent LE (-1.191 kcal/mol/HA)
✓ Good fit quality (FQ -9.76)
✓ Strong H-bond network (10 bonds)
✓ Deep burial (87% SASA buried)
✓ Lipophilic contacts well-matched (72%)
✗ Moderate strain (9.7 kcal/mol)
✗ Geometry warnings
✗ Internal clashes (9)
Score
-22.634
kcal/mol
LE
-1.191
kcal/mol/HA
Fit Quality
-9.76
FQ (Leeson)
HAC
19
heavy atoms
MW
254
Da
LogP
2.00
cLogP
Interaction summary
HB 10
HY 10
PI 2
CLASH 5
Interaction summary
HB 10
HY 10
PI 2
CLASH 5
| Final rank | 2.989 | Score | -22.634 |
|---|---|---|---|
| Inter norm | -1.295 | Intra norm | 0.104 |
| Top1000 | no | Excluded | no |
| Contacts | 15 | H-bonds | 10 |
| Artifact reason | geometry warning; 9 clashes; 2 protein clashes | ||
| Residues |
ASN103
HIS102
MET98
TYR94
ARG113
ASP10
CYS69
GLY70
GLY72
GLY74
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 | 10 | Native recall | 0.71 |
| Jaccard | 0.53 | 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 599 | 1.774607054232465 | -1.34971 | -23.3525 | 7 | 13 | 0 | 0.00 | 0.00 | - | no | Open |
| 626 | 2.9890510231618737 | -1.2951 | -22.6337 | 10 | 15 | 10 | 0.71 | 0.33 | - | no | Current |
| 609 | 3.0159037591829456 | -1.44252 | -25.0979 | 8 | 12 | 0 | 0.00 | 0.00 | - | no | Open |
| 624 | 3.0872971814603587 | -1.32537 | -23.3887 | 7 | 13 | 0 | 0.00 | 0.00 | - | no | Open |
| 618 | 3.1835171244642915 | -1.27025 | -21.0326 | 7 | 13 | 0 | 0.00 | 0.00 | - | no | Open |
| 600 | 3.7608836455983226 | -1.51756 | -26.9668 | 8 | 14 | 0 | 0.00 | 0.00 | - | no | Open |
| 620 | 3.8864306304714464 | -1.45494 | -23.8158 | 7 | 16 | 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
-22.634kcal/mol
Ligand efficiency (LE)
-1.1912kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-9.764
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
19HA
Physicochemical properties
Molecular weight
254.2Da
Lipinski: ≤ 500 Da
LogP (cLogP)
2.00
Lipinski: ≤ 5
Rotatable bonds
3
Conformational strain (MMFF94s)
Strain energy (ΔE)
9.70kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
32.81kcal/mol
Minimised FF energy
23.11kcal/mol
SASA & burial
✓ computed
SASA (unbound)
459.5Ų
Total solvent-accessible surface area of free ligand
BSA total
398.4Ų
Buried surface area upon binding
BSA apolar
285.4Ų
Hydrophobic contacts buried
BSA polar
113.1Ų
Polar contacts buried
Fraction buried
86.7%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
71.6%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-2056.9Ų
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
769.4Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)