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 high
Native strong
SASA done
Strain ΔE
17.5 kcal/mol
Protein clashes
1
Internal clashes
1
Native overlap
contact recall 0.93, Jaccard 0.81, H-bond role recall 0.67
Reason: no major geometry red flags detected
1 protein-contact clashes
58% of hydrophobic surface appears solvent-exposed (14/24 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 (-0.607 kcal/mol/HA)
✓ Good fit quality (FQ -5.92)
✓ Strong H-bond network (12 bonds)
✓ Good burial (61% SASA buried)
✓ Lipophilic contacts well-matched (76%)
✗ Moderate strain (17.5 kcal/mol)
✗ Geometry warnings
✗ Many internal clashes (13)
Score
-18.827
kcal/mol
LE
-0.607
kcal/mol/HA
Fit Quality
-5.92
FQ (Leeson)
HAC
31
heavy atoms
MW
424
Da
LogP
3.89
cLogP
Interaction summary
HB 12
HY 9
PI 4
CLASH 1
⚠ Exposure 58%
Interaction summary
HB 12
HY 9
PI 4
CLASH 1
⚠ Exposure 58%
Partial hydrophobic solvent exposure
58% of hydrophobic surface appears solvent-exposed (14/24 atoms). Partial exposure is common but may limit selectivity and membrane permeability.
Non-polar atoms 24
Buried (contacted) 10
Exposed 14
LogP 3.89
H-bonds 12
Exposed fragments:
phenyl (6/6 atoms exposed)phenyl (5/6 atoms exposed)aliphatic chain/group (5 atoms exposed)
| Final rank | 4.113 | Score | -18.827 |
|---|---|---|---|
| Inter norm | -0.859 | Intra norm | 0.252 |
| Top1000 | no | Excluded | no |
| Contacts | 15 | H-bonds | 12 |
| Artifact reason | geometry warning; 13 clashes; 2 protein clashes | ||
| Residues |
ARG137
ARG141
ASN103
HIS102
MET98
ASP10
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 | 13 | Native recall | 0.93 |
| Jaccard | 0.81 | RMSD | - |
| HB strict | 7 | Strict recall | 0.58 |
| HB same residue+role | 6 | HB role recall | 0.67 |
| HB same residue | 6 | HB residue recall | 0.75 |
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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 259 | 2.186616249521787 | -0.767138 | -19.682 | 6 | 18 | 0 | 0.00 | 0.00 | - | no | Open |
| 249 | 2.4030765412283297 | -0.909145 | -25.0763 | 5 | 13 | 0 | 0.00 | 0.00 | - | no | Open |
| 269 | 2.6372940514961205 | -1.01685 | -23.5396 | 9 | 22 | 0 | 0.00 | 0.00 | - | no | Open |
| 312 | 3.2393473524780756 | -0.83684 | -17.5204 | 10 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 288 | 3.272332131596446 | -0.77267 | -17.6481 | 3 | 14 | 0 | 0.00 | 0.00 | - | no | Open |
| 312 | 3.6488397918246784 | -0.752019 | -16.7004 | 7 | 19 | 0 | 0.00 | 0.00 | - | no | Open |
| 266 | 3.7498473298653865 | -0.798347 | -21.5987 | 5 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 288 | 4.113009301054676 | -0.859307 | -18.827 | 12 | 15 | 13 | 0.93 | 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
-18.827kcal/mol
Ligand efficiency (LE)
-0.6073kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-5.917
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
31HA
Physicochemical properties
Molecular weight
423.5Da
Lipinski: ≤ 500 Da
LogP (cLogP)
3.89
Lipinski: ≤ 5
Rotatable bonds
8
Conformational strain (MMFF94s)
Strain energy (ΔE)
17.54kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
52.82kcal/mol
Minimised FF energy
35.28kcal/mol
SASA & burial
✓ computed
SASA (unbound)
696.1Ų
Total solvent-accessible surface area of free ligand
BSA total
421.6Ų
Buried surface area upon binding
BSA apolar
320.7Ų
Hydrophobic contacts buried
BSA polar
100.9Ų
Polar contacts buried
Fraction buried
60.6%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
76.1%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-2293.5Ų
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
761.3Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)