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
18.1 kcal/mol
Protein clashes
2
Internal clashes
2
Native overlap
contact recall 0.76, Jaccard 0.67, H-bond role recall 0.45
Reason: no major geometry red flags detected
2 protein-contact clashes
44% of hydrophobic surface appears solvent-exposed (11/25 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 (-0.960 kcal/mol/HA)
✓ Good fit quality (FQ -9.68)
✓ Strong H-bond network (10 bonds)
✓ Deep burial (80% SASA buried)
✓ Lipophilic contacts well-matched (78%)
✗ Moderate strain (18.1 kcal/mol)
✗ Geometry warnings
✗ Many internal clashes (15)
Score
-33.595
kcal/mol
LE
-0.960
kcal/mol/HA
Fit Quality
-9.68
FQ (Leeson)
HAC
35
heavy atoms
MW
490
Da
LogP
3.21
cLogP
Interaction summary
HB 10
HY 13
PI 1
CLASH 2
⚠ Exposure 44%
Interaction summary
HB 10
HY 13
PI 1
CLASH 2
⚠ Exposure 44%
Partial hydrophobic solvent exposure
44% of hydrophobic surface appears solvent-exposed (11/25 atoms). Partial exposure is common but may limit selectivity and membrane permeability.
Non-polar atoms 25
Buried (contacted) 14
Exposed 11
LogP 3.21
H-bonds 10
Exposed fragments:
phenyl (6/6 atoms exposed)phenyl (4/6 atoms exposed)aliphatic chain/group (1 atom exposed)
| Final rank | 4.125 | Score | -33.595 |
|---|---|---|---|
| Inter norm | -0.920 | Intra norm | -0.040 |
| Top1000 | no | Excluded | no |
| Contacts | 19 | H-bonds | 10 |
| Artifact reason | geometry warning; 15 clashes; 2 protein clashes | ||
| Residues |
ALA158
ALA24
ALA40
ASN126
ASN41
ASP129
GLU73
GLY23
GLY25
GLY71
LYS127
LYS159
LYS26
PHE38
SER157
SER27
SER28
THR44
THR69
| ||
Protein summary
165 residues
| Protein target | T22 | Atoms | 2561 |
|---|---|---|---|
| Residues | 165 | Chains | 1 |
| Residue summary | LEU:363; LYS:242; ALA:231; ARG:214; ILE:190; GLU:180; VAL:144; SER:143; PHE:140; ASN:112; THR:112; TYR:105; GLN:102; ASP:96; GLY:77; TRP:48 | ||
Native ligand reference
★ reference
Interaction fingerprint calculated directly from the uploaded native ligand without docking. Current H-bond mode: strict.
| Name | RAB5A | Contacts | 21 |
|---|---|---|---|
| Pose | Open native pose | HB | 0 |
| IFP residues |
ALA158
ALA24
ALA40
ASN126
ASN41
ASP129
GLN42
GLU21
GLU73
GLY23
GLY25
LEU130
LEU39
LYS127
LYS159
LYS26
PHE38
SER157
SER22
SER27
SER28
| ||
| Current overlap | 16 | Native recall | 0.76 |
| Jaccard | 0.67 | RMSD | - |
| HB strict | 7 | Strict recall | 0.47 |
| HB same residue+role | 5 | HB role recall | 0.45 |
| HB same residue | 5 | HB residue recall | 0.45 |
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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 528 | 2.1387138988154137 | -0.609177 | -24.6017 | 5 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 554 | 3.0340948021098755 | -0.676873 | -24.202 | 4 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 502 | 4.044125737962072 | -0.738563 | -24.401 | 3 | 13 | 0 | 0.00 | 0.00 | - | no | Open |
| 501 | 4.125457344917445 | -0.9198 | -33.5948 | 10 | 19 | 16 | 0.76 | 0.45 | - | no | Current |
| 481 | 4.413251044837232 | -0.98789 | -30.3095 | 5 | 22 | 0 | 0.00 | 0.00 | - | no | Open |
| 500 | 4.744143382506253 | -0.613518 | -18.2226 | 5 | 14 | 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
-33.595kcal/mol
Ligand efficiency (LE)
-0.9599kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-9.681
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
35HA
Physicochemical properties
Molecular weight
489.6Da
Lipinski: ≤ 500 Da
LogP (cLogP)
3.21
Lipinski: ≤ 5
Rotatable bonds
6
Conformational strain (MMFF94s)
Strain energy (ΔE)
18.11kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
33.45kcal/mol
Minimised FF energy
15.34kcal/mol
SASA & burial
✓ computed
SASA (unbound)
768.7Ų
Total solvent-accessible surface area of free ligand
BSA total
611.6Ų
Buried surface area upon binding
BSA apolar
474.9Ų
Hydrophobic contacts buried
BSA polar
136.8Ų
Polar contacts buried
Fraction buried
79.6%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
77.6%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-1462.3Ų
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
1368.5Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA
535.2Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)