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
19.6 kcal/mol
Protein clashes
1
Internal clashes
1
Native overlap
contact recall 0.79, Jaccard 0.61, H-bond role recall 0.67
Reason: no major geometry red flags detected
1 protein-contact clashes
47% of hydrophobic surface appears solvent-exposed (9/19 atoms). Partial exposure is common but may limit selectivity and membrane permeability.
Molecular report
Promising
Reasonable quality metrics. Warrants further investigation.
✓ Excellent LE (-0.885 kcal/mol/HA)
✓ Good fit quality (FQ -8.26)
✓ Strong H-bond network (11 bonds)
✓ Deep burial (67% SASA buried)
✓ Lipophilic contacts well-matched (65%)
✗ Moderate strain (19.6 kcal/mol)
✗ Geometry warnings
✗ Internal clashes (6)
Score
-23.907
kcal/mol
LE
-0.885
kcal/mol/HA
Fit Quality
-8.26
FQ (Leeson)
HAC
27
heavy atoms
MW
401
Da
LogP
3.74
cLogP
Interaction summary
HB 11
HY 2
PI 3
CLASH 1
⚠ Exposure 47%
Interaction summary
HB 11
HY 2
PI 3
CLASH 1
⚠ Exposure 47%
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
Partial hydrophobic solvent exposure
47% of hydrophobic surface appears solvent-exposed (9/19 atoms). Partial exposure is common but may limit selectivity and membrane permeability.
Non-polar atoms 19
Buried (contacted) 10
Exposed 9
LogP 3.74
H-bonds 11
Exposed fragments:
phenyl (4/5 atoms exposed)phenyl (6/6 atoms exposed)aliphatic chain/group (1 atom exposed)
| Final rank | 4.132 | Score | -23.907 |
|---|---|---|---|
| Inter norm | -0.954 | Intra norm | 0.069 |
| Top1000 | no | Excluded | no |
| Contacts | 15 | H-bonds | 11 |
| Artifact reason | geometry warning; 6 clashes; 3 protein clashes | ||
| Residues |
ARG137
ARG141
ASN103
HIS102
MET98
SER99
CYS69
GLY70
GLY72
GLY74
HIS11
ILE73
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 | 11 | Native recall | 0.79 |
| Jaccard | 0.61 | RMSD | - |
| HB strict | 8 | Strict recall | 0.67 |
| HB same residue+role | 6 | HB role recall | 0.67 |
| HB same residue | 5 | HB residue recall | 0.62 |
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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 569 | 0.36532912233574083 | -1.30221 | -32.7212 | 7 | 19 | 0 | 0.00 | 0.00 | - | no | Open |
| 569 | 2.3737859879803827 | -0.913048 | -17.8893 | 7 | 13 | 0 | 0.00 | 0.00 | - | no | Open |
| 589 | 2.791741137083932 | -1.08787 | -23.2147 | 6 | 17 | 0 | 0.00 | 0.00 | - | no | Open |
| 599 | 3.8312358695408832 | -0.914807 | -24.99 | 8 | 17 | 0 | 0.00 | 0.00 | - | no | Open |
| 562 | 3.9390179097197437 | -1.12619 | -30.2577 | 9 | 19 | 0 | 0.00 | 0.00 | - | no | Open |
| 598 | 4.131557866139451 | -0.953971 | -23.907 | 11 | 15 | 11 | 0.79 | 0.67 | - | no | Current |
Molecular metrics
RDKit SASA burial, strain energy (MMFF94s), ligand efficiency and fit quality for this docking pose.
Scoring & efficiency
Docking score
-23.907kcal/mol
Ligand efficiency (LE)
-0.8854kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-8.261
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
27HA
Physicochemical properties
Molecular weight
400.8Da
Lipinski: ≤ 500 Da
LogP (cLogP)
3.74
Lipinski: ≤ 5
Rotatable bonds
4
Conformational strain (MMFF94s)
Strain energy (ΔE)
19.60kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
-53.45kcal/mol
Minimised FF energy
-73.05kcal/mol
SASA & burial
✓ computed
SASA (unbound)
629.1Ų
Total solvent-accessible surface area of free ligand
BSA total
421.0Ų
Buried surface area upon binding
BSA apolar
272.4Ų
Hydrophobic contacts buried
BSA polar
148.6Ų
Polar contacts buried
Fraction buried
66.9%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
64.7%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-2130.9Ų
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
829.2Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)