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
Weak
SASA cached
Weak or marginal quality
Binding strong
Geometry high
Native strong
SASA done
Strain ΔE
10.3 kcal/mol
Protein clashes
1
Internal clashes
1
Native overlap
contact recall 0.79, Jaccard 0.69, H-bond role recall 0.22
Reason: no major geometry red flags detected
1 protein-contact clashes
56% of hydrophobic surface appears solvent-exposed (14/25 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 (-0.860 kcal/mol/HA)
✓ Good fit quality (FQ -8.38)
✓ Strong H-bond network (8 bonds)
✓ Good burial (65% SASA buried)
✓ Lipophilic contacts well-matched (82%)
✗ Moderate strain (10.3 kcal/mol)
✗ Geometry warnings
✗ Many internal clashes (14)
Score
-26.666
kcal/mol
LE
-0.860
kcal/mol/HA
Fit Quality
-8.38
FQ (Leeson)
HAC
31
heavy atoms
MW
423
Da
LogP
5.66
cLogP
Interaction summary
HB 8
HY 3
PI 4
CLASH 1
⚠ Exposure 56%
Interaction summary
HB 8
HY 3
PI 4
CLASH 1
⚠ Exposure 56%
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
56% of hydrophobic surface appears solvent-exposed (14/25 atoms). Partial exposure is common but may limit selectivity and membrane permeability.
Non-polar atoms 25
Buried (contacted) 11
Exposed 14
LogP 5.66
H-bonds 8
Exposed fragments:
phenyl (6/6 atoms exposed)phenyl (6/6 atoms exposed)aliphatic chain/group (2 atoms exposed)
| Final rank | 3.725 | Score | -26.666 |
|---|---|---|---|
| Inter norm | -0.825 | Intra norm | -0.035 |
| Top1000 | no | Excluded | no |
| Contacts | 13 | H-bonds | 8 |
| Artifact reason | geometry warning; 14 clashes; 2 protein clashes | ||
| Residues |
ARG137
ARG140
ARG141
ASN103
HIS102
HIS138
CYS69
GLY70
HIS11
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 | 11 | Native recall | 0.79 |
| Jaccard | 0.69 | RMSD | - |
| HB strict | 4 | Strict recall | 0.33 |
| HB same residue+role | 2 | HB role recall | 0.22 |
| HB same residue | 2 | HB residue recall | 0.25 |
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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 439 | 1.1628233344151113 | -0.906918 | -27.9879 | 3 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 468 | 1.2633865118385668 | -0.898731 | -27.8853 | 2 | 17 | 0 | 0.00 | 0.00 | - | no | Open |
| 366 | 2.346994116576859 | -1.13989 | -35.9598 | 5 | 19 | 0 | 0.00 | 0.00 | - | no | Open |
| 432 | 2.981404368719356 | -0.687014 | -21.8499 | 4 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 385 | 3.6381866787315404 | -0.739509 | -19.1107 | 3 | 18 | 0 | 0.00 | 0.00 | - | no | Open |
| 422 | 3.724908937099832 | -0.82493 | -26.6656 | 8 | 13 | 11 | 0.79 | 0.22 | - | no | Current |
| 386 | 3.85148268722908 | -0.870285 | -26.6452 | 10 | 13 | 0 | 0.00 | 0.00 | - | no | Open |
| 393 | 4.116103612653292 | -0.926482 | -28.3794 | 10 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 376 | 4.356730612096464 | -0.774795 | -20.8823 | 13 | 14 | 0 | 0.00 | 0.00 | - | no | Open |
| 416 | 4.907697742604002 | -0.626708 | -19.1249 | 3 | 10 | 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
-26.666kcal/mol
Ligand efficiency (LE)
-0.8602kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-8.380
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
31HA
Physicochemical properties
Molecular weight
422.5Da
Lipinski: ≤ 500 Da
LogP (cLogP)
5.66
Lipinski: ≤ 5
Rotatable bonds
6
Conformational strain (MMFF94s)
Strain energy (ΔE)
10.27kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
107.14kcal/mol
Minimised FF energy
96.87kcal/mol
SASA & burial
✓ computed
SASA (unbound)
684.1Ų
Total solvent-accessible surface area of free ligand
BSA total
445.0Ų
Buried surface area upon binding
BSA apolar
364.6Ų
Hydrophobic contacts buried
BSA polar
80.5Ų
Polar contacts buried
Fraction buried
65.0%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
81.9%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-2282.9Ų
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
782.1Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)